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3. Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima at 1.7 A resolution

Author

Schwarzenbacher, R, Deacon, AM, Jaroszewski, L, Brinen, LS, Canaves, JM, Dai, X, Elsliger, MA, Floyd, R, Godzik, A, Grittini, C, Grzechnik, SK, Klock, HE, Koesema, E, Kovarik, JS, Kreusch, A, Kuhn, P, Lesley, SA, McMullan, D, McPhillips, TM, Miller, MD, Morse, A, Moy, K, Nelson, MS, Ouyang, J, Page, R, Robb, A, Quijano, K, Spraggon, G, Stevens, RC, van den Bedem, H, Velasquez, J, Vincent, J, von Delft, F, Wang, X, West, B, Wolf, G, Hodgson, KO, Wooley, J, and Wilson, IA

Subjects
Models, Molecular, Protein Conformation, Molecular Sequence Data, Reproducibility of Results, Thermotoga maritima, Amino Acid Sequence, Crystallography, X-Ray
Published
2004

4. RNAi Screen Indicates Widespread Biological Function for Human Natural Antisense Transcripts

Author

Gruner, AC, Faghihi, MA, Kocerha, J, Modarresi, F, Engstroem, PG, Chalk, AM, Brothers, SP, Koesema, E, St Laurent, G, Wahlestedt, C, Gruner, AC, Faghihi, MA, Kocerha, J, Modarresi, F, Engstroem, PG, Chalk, AM, Brothers, SP, Koesema, E, St Laurent, G, and Wahlestedt, C

Abstract

Natural antisense transcripts represent a class of regulatory RNA molecules, which are characterized by their complementary sequence to another RNA transcript. Extensive sequencing efforts suggest that natural antisense transcripts are prevalent throughout the mammalian genome; however, their biological significance has not been well defined. We performed a loss-of-function RNA interference (RNAi) screen, which targeted 797 evolutionary conserved antisense transcripts, and found evidence for a regulatory role for a number of natural antisense transcripts. Specifically, we found that natural antisense transcripts for CCPG1 and RAPGEF3 may functionally disrupt signaling pathways and corresponding biological phenotypes, such as cell viability, either independently or in parallel with the corresponding sense transcript. Our results show that the large-scale siRNA screen can be applied to evaluate natural antisense transcript modulation of fundamental cellular events.

Published
2010

5. Genome-wide Insertional mutagenesis of Arabidopsis thaliana

Author

Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H. M., Shinn, P., Stevenson, D. K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C. C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D. E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W. L., Berry, C. C., Ecker, J. R., Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H. M., Shinn, P., Stevenson, D. K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C. C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D. E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W. L., Berry, C. C., and Ecker, J. R.

Abstract

Times Cited: 2876

Published
2003

6. STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE

Author

Spraggon, G., primary, Koesema, E., additional, Scarselli, M., additional, Malito, E., additional, Biagini, M., additional, Norais, N., additional, Emolo, C., additional, Barocchi, M.A., additional, Giusti, F., additional, Hilleringmann, M., additional, Rappuoli, R., additional, Lesley, S., additional, Covacci, A., additional, Masignani, V., additional, and Ferlenghi, I., additional

Published
2010
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7. Synthesis and Screening of a DNA-Encoded Library of Non-Peptidic Macrocycles.

Author

Koesema E, Roy A, Paciaroni NG, Coito C, Tokmina-Roszyk M, and Kodadek T

Subjects
Combinatorial Chemistry Techniques, Gene Library, Ligands, DNA chemistry, Solid-Phase Synthesis Techniques methods
Abstract

There is considerable interest in the development of libraries of non-peptidic macrocycles as a source of ligands for difficult targets. We report here the solid-phase synthesis of a DNA-encoded library of several hundred thousand thioether-linked macrocycles. The library was designed to be highly diverse with respect to backbone scaffold diversity and to minimize the number of amide N-H bonds, which compromise cell permeability. The utility of the library as a source of protein ligands is demonstrated through the isolation of compounds that bind Streptavidin, a model target, with high affinity., (© 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Published
2022
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8. High-Throughput Quality Control Assay for the Solid-Phase Synthesis of DNA-Encoded Libraries of Macrocycles*.

Author

Roy A, Koesema E, and Kodadek T

Subjects
Cyclization, Sulfides chemical synthesis, DNA chemistry, Immobilized Nucleic Acids chemistry, Macrocyclic Compounds chemical synthesis, Solid-Phase Synthesis Techniques methods
Abstract

There is considerable interest in the development of libraries of scaffold-diverse macrocycles as a source of ligands for difficult targets, such as protein-protein interaction surfaces. A classic problem in the synthesis of high-quality macrocyclic libraries is that some linear precursors will cyclize efficiently while some will not, depending on their conformational preferences. We report here a powerful quality control method that can be employed to readily distinguish between scaffolds that do and do not cyclize efficiently during solid-phase synthesis of thioether macrocycles without the need for tedious liquid chromatography/mass spectrometry analysis. We demonstrate that this assay can be employed to identify linear impurities in a DNA-encoded library of macrocycles. We also use the method to establish a useful quality control protocol for re-synthesis of putative macrocyclic screening hits., (© 2021 Wiley-VCH GmbH.)

Published
2021
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9. Global analysis of gene expression mediated by OX1 orexin receptor signaling in a hypothalamic cell line.

Author

Koesema E and Kodadek T

Subjects
Animals, CHO Cells, Cell Line, Cricetulus, Hippocampus cytology, Humans, Orexin Receptors metabolism, Orexins metabolism, Sequence Analysis, RNA, Sleep Deprivation genetics, Transcription Factors metabolism, Gene Expression physiology, Hippocampus metabolism, Orexin Receptors physiology, Signal Transduction
Abstract

The orexins and their cognate G-protein coupled receptors have been widely studied due to their associations with various behaviors and cellular processes. However, the detailed downstream signaling cascades that mediate these effects are not completely understood. We report the generation of a neuronal model cell line that stably expresses the OX1 orexin receptor (OX1) and an RNA-Seq analysis of changes in gene expression seen upon receptor activation. Upon treatment with orexin, several families of related transcription factors are transcriptionally regulated, including the early growth response genes (Egr), the Kruppel-like factors (Klf), and the Nr4a subgroup of nuclear hormone receptors. Furthermore, some of the transcriptional effects observed have also been seen in data from in vivo sleep deprivation microarray studies, supporting the physiological relevance of the data set. Additionally, inhibition of one of the most highly regulated genes, serum and glucocorticoid-regulated kinase 1 (Sgk1), resulted in the diminished orexin-dependent induction of a subset of genes. These results provide new insight into the molecular signaling events that occur during OX1 signaling and support a role for orexin signaling in the stimulation of wakefulness during sleep deprivation studies.

Published
2017
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10. RNAi screen indicates widespread biological function for human natural antisense transcripts.

Author

Faghihi MA, Kocerha J, Modarresi F, Engström PG, Chalk AM, Brothers SP, Koesema E, St Laurent G, and Wahlestedt C

Subjects
Cell Line, Cell Proliferation, Gene Knockdown Techniques, Humans, Oligonucleotide Array Sequence Analysis, RNA Interference, RNA, Antisense genetics, RNA, Messenger genetics
Abstract

Natural antisense transcripts represent a class of regulatory RNA molecules, which are characterized by their complementary sequence to another RNA transcript. Extensive sequencing efforts suggest that natural antisense transcripts are prevalent throughout the mammalian genome; however, their biological significance has not been well defined. We performed a loss-of-function RNA interference (RNAi) screen, which targeted 797 evolutionary conserved antisense transcripts, and found evidence for a regulatory role for a number of natural antisense transcripts. Specifically, we found that natural antisense transcripts for CCPG1 and RAPGEF3 may functionally disrupt signaling pathways and corresponding biological phenotypes, such as cell viability, either independently or in parallel with the corresponding sense transcript. Our results show that the large-scale siRNA screen can be applied to evaluate natural antisense transcript modulation of fundamental cellular events.

Published
2010
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11. Supramolecular organization of the repetitive backbone unit of the Streptococcus pneumoniae pilus.

Author

Spraggon G, Koesema E, Scarselli M, Malito E, Biagini M, Norais N, Emolo C, Barocchi MA, Giusti F, Hilleringmann M, Rappuoli R, Lesley S, Covacci A, Masignani V, and Ferlenghi I

Subjects
Amino Acid Sequence, Bacterial Proteins chemistry, Crystallography, X-Ray, Microscopy, Electron, Transmission, Models, Molecular, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Fimbriae, Bacterial, Streptococcus pneumoniae metabolism
Abstract

Streptococcus pneumoniae, like many other Gram-positive bacteria, assembles long filamentous pili on their surface through which they adhere to host cells. Pneumococcal pili are formed by a backbone, consisting of the repetition of the major component RrgB, and two accessory proteins (RrgA and RrgC). Here we reconstruct by transmission electron microscopy and single particle image reconstruction method the three dimensional arrangement of two neighbouring RrgB molecules, which represent the minimal repetitive structural domain of the native pilus. The crystal structure of the D2-D4 domains of RrgB was solved at 1.6 A resolution. Rigid-body fitting of the X-ray coordinates into the electron density map enabled us to define the arrangement of the backbone subunits into the S. pneumoniae native pilus. The quantitative fitting provide evidence that the pneumococcal pilus consists uniquely of RrgB monomers assembled in a head-to-tail organization. The presence of short intra-subunit linker regions connecting neighbouring domains provides the molecular basis for the intrinsic pilus flexibility.

Published
2010
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12. Screening the mammalian extracellular proteome for regulators of embryonic human stem cell pluripotency.

Author

Gonzalez R, Jennings LL, Knuth M, Orth AP, Klock HE, Ou W, Feuerhelm J, Hull MV, Koesema E, Wang Y, Zhang J, Wu C, Cho CY, Su AI, Batalov S, Chen H, Johnson K, Laffitte B, Nguyen DG, Snyder EY, Schultz PG, Harris JL, and Lesley SA

Subjects
Embryonic Stem Cells cytology, Embryonic Stem Cells drug effects, Genome-Wide Association Study, High-Throughput Screening Assays, Humans, Mitogen-Activated Protein Kinase 3 genetics, Mitogen-Activated Protein Kinase 3 metabolism, Octamer Transcription Factor-3 genetics, Pluripotent Stem Cells cytology, Pluripotent Stem Cells drug effects, Proteome genetics, Receptors, Neuropeptide genetics, Receptors, Neuropeptide metabolism, Signal Transduction, Embryonic Stem Cells metabolism, Octamer Transcription Factor-3 metabolism, Pluripotent Stem Cells metabolism, Proteome metabolism
Abstract

Approximately 3,500 mammalian genes are predicted to be secreted or single-pass transmembrane proteins. The function of the majority of these genes is still unknown, and a number of the encoded proteins might find use as new therapeutic agents themselves or as targets for small molecule or antibody drug development. To analyze the physiological activities of the extracellular proteome, we developed a large-scale, high-throughput protein expression, purification, and screening platform. For this study, the complete human extracellular proteome was analyzed and prioritized based on genome-wide disease association studies to select 529 initial target genes. These genes were cloned into three expression vectors as native sequences and as N-terminal and C-terminal Fc fusions to create an initial collection of 806 purified secreted proteins. To determine its utility, this library was screened in an OCT4-based cellular assay to identify regulators of human embryonic stem-cell self-renewal. We found that the pigment epithelium-derived factor can promote long-term pluripotent growth of human embryonic stem cells without bFGF or TGFbeta/Activin/Nodal ligand supplementation. Our results further indicate that activation of the pigment epithelium-derived factor receptor-Erk1/2 signaling pathway by the pigment epithelium-derived factor is sufficient to maintain the self-renewal of pluripotent human embryonic stem cells. These experiments illustrate the potential for discovering novel biological functions by directly screening protein diversity in cell-based phenotypic or reporter assays.

Published
2010
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13. Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold.

Author

Kozbial P, Xu Q, Chiu HJ, McMullan D, Krishna SS, Miller MD, Abdubek P, Acosta C, Astakhova T, Axelrod HL, Carlton D, Clayton T, Deller M, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Murphy KD, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Spraggon G, Trout CV, van den Bedem H, Weekes D, White A, Wolf G, Zubieta C, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Protein Folding
Published
2008
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14. Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution.

Author

Axelrod HL, McMullan D, Krishna SS, Miller MD, Elsliger MA, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Crystallization, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Thermotoga maritima enzymology, Hydroxymethyl and Formyl Transferases chemistry, Multienzyme Complexes chemistry, Nucleotide Deaminases chemistry
Published
2008
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15. Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution.

Author

Mathews II, McMullan D, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K, Rife CL, Schwarzenbacher R, Spraggon G, Stevens RC, van den Bedem H, Weekes D, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, Molecular Sequence Data, Protein Conformation, Sequence Homology, Amino Acid, Phosphotransferases (Alcohol Group Acceptor) chemistry, Thermotoga maritima enzymology
Published
2008
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16. Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 angstroms resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate.

Author

Xu Q, Saikatendu KS, Krishna SS, McMullan D, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Miller MD, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Schwarzenbacher R, van den Bedem H, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins chemistry, Bacterial Proteins physiology, Crystallography, X-Ray, Hydrolysis, Molecular Sequence Data, Organophosphates chemistry, Thioglycosides chemistry, Bacillus subtilis enzymology, Organophosphates metabolism, Phosphoric Monoester Hydrolases chemistry, Phosphoric Monoester Hydrolases physiology, Thioglycosides metabolism
Published
2007
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17. Crystal structure of NMA1982 from Neisseria meningitidis at 1.5 angstroms resolution provides a structural scaffold for nonclassical, eukaryotic-like phosphatases.

Author

Krishna SS, Tautz L, Xu Q, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Morse AT, Mustelin T, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Motifs, Amino Acid Sequence, Bacterial Proteins metabolism, Bacterial Proteins physiology, Binding Sites, Crystallography, X-Ray, Molecular Sequence Data, Phosphoric Monoester Hydrolases metabolism, Phosphoric Monoester Hydrolases physiology, Protein Structure, Secondary, Bacterial Proteins chemistry, Neisseria meningitidis enzymology, Phosphoric Monoester Hydrolases chemistry
Published
2007
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18. Crystal structure of homoserine O-succinyltransferase from Bacillus cereus at 2.4 A resolution.

Author

Zubieta C, Krishna SS, McMullan D, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Deller M, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kumar A, Marciano D, Morse AT, Nigoghossian E, Oommachen S, Reyes R, Rife CL, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins chemistry, Crystallography, X-Ray, Dimerization, Haemophilus influenzae enzymology, Models, Molecular, Molecular Sequence Data, Protein Conformation, Bacillus cereus enzymology, Homoserine O-Succinyltransferase chemistry
Published
2007
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19. Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function.

Author

Premkumar L, Rife CL, Sri Krishna S, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Floyd R, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kovarik JS, Kreusch A, Levin I, McPhillips TM, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rezezadeh F, Rodionov D, Schwarzenbacher R, Spraggon G, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins genetics, Crystallography, X-Ray, Molecular Sequence Data, Repressor Proteins genetics, Sequence Analysis, DNA, Thermotoga maritima genetics, Bacterial Proteins chemistry, Models, Molecular, Repressor Proteins chemistry, Thermotoga maritima chemistry
Published
2007
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20. Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution.

Author

Weekes D, Miller MD, Krishna SS, McMullan D, McPhillips TM, Acosta C, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Morse AT, Quijano K, Spraggon G, van den Bedem H, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallization, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, DNA-Binding Proteins chemistry, Thermotoga maritima chemistry, Transcription Factors chemistry
Published
2007
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21. Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p.

Author

Xu Q, Krishna SS, McMullan D, Schwarzenbacher R, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins isolation & purification, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Folding, Protein Structure, Secondary, Saccharomyces cerevisiae Proteins chemistry, Thermotoga maritima chemistry, ran GTP-Binding Protein chemistry, Bacterial Proteins chemistry, Thermotoga maritima enzymology
Published
2006
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22. Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution.

Author

Kosloff M, Han GW, Krishna SS, Schwarzenbacher R, Fasnacht M, Elsliger MA, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Feuerhelm J, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Johnson H, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Levin I, McMullan D, Miller MD, Morse AT, Moy K, Nigoghossian E, Okach L, Oommachen S, Page R, Paulsen J, Quijano K, Reyes R, Rife CL, Sims E, Spraggon G, Sridhar V, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Agrobacterium tumefaciens chemistry, Agrobacterium tumefaciens cytology, Amino Acid Sequence, Bacterial Proteins classification, Crystallography, X-Ray, Dimerization, Glutathione Transferase classification, Models, Molecular, Molecular Sequence Data, Phylogeny, Protein Structure, Secondary, Agrobacterium tumefaciens enzymology, Bacterial Proteins chemistry, Glutathione Transferase chemistry
Abstract

Glutathione S-transferases (GSTs) comprise a diverse superfamily of enzymes found in organisms from all kingdoms of life. GSTs are involved in diverse processes, notably small-molecule biosynthesis or detoxification, and are frequently also used in protein engineering studies or as biotechnology tools. Here, we report the high-resolution X-ray structure of Atu5508 from the pathogenic soil bacterium Agrobacterium tumefaciens (atGST1). Through use of comparative sequence and structural analysis of the GST superfamily, we identified local sequence and structural signatures, which allowed us to distinguish between different GST classes. This approach enables GST classification based on structure, without requiring additional biochemical or immunological data. Consequently, analysis of the atGST1 crystal structure suggests a new GST class, distinct from previously characterized GSTs, which would make it an attractive target for further biochemical studies., ((c) 2006 Wiley-Liss, Inc.)

Published
2006
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23. Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site.

Author

DiDonato M, Krishna SS, Schwarzenbacher R, McMullan D, Agarwalla S, Brittain SM, Miller MD, Abdubek P, Ambing E, Axelrod HL, Canaves JM, Chiu HJ, Deacon AM, Duan L, Elsliger MA, Godzik A, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Acid Phosphatase isolation & purification, Amino Acid Sequence, Binding Sites, Clostridium acetobutylicum chemistry, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Folding, Acid Phosphatase chemistry, Clostridium acetobutylicum enzymology
Published
2006
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24. Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold.

Author

Schwarzenbacher R, McMullan D, Krishna SS, Xu Q, Miller MD, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, McPhillips TM, Morse AT, Quijano K, Spraggon G, Stevens RC, van den Bedem H, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins chemistry, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Protein Folding, Phosphotransferases (Alcohol Group Acceptor) chemistry, Thermotoga maritima enzymology
Published
2006
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25. Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution.

Author

Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Jaroszewski L, Miller MD, Abdubek P, Agarwalla S, Ambing E, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Grzechnik SK, Hale J, Hampton E, Haugen J, Jin KK, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Levin I, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins chemistry, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Protein Structure, Quaternary, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor chemistry, Thermotoga maritima enzymology
Published
2006
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26. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution.

Author

Han GW, Sri Krishna S, Schwarzenbacher R, McMullan D, Ginalski K, Elsliger MA, Brittain SM, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod H, Canaves JM, Chiu HJ, DiDonato M, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Miller MD, Morse AT, Moy K, Nigoghossian E, Oommachen S, Ouyang J, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Crystallization, Crystallography, X-Ray, Molecular Sequence Data, Sequence Alignment, Bacterial Proteins chemistry, Lipoproteins chemistry, Thermotoga maritima chemistry
Published
2006
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27. Crystal structure of the human TRPV2 channel ankyrin repeat domain.

Author

McCleverty CJ, Koesema E, Patapoutian A, Lesley SA, and Kreusch A

Subjects
Amino Acid Sequence, Binding Sites, Humans, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Ankyrin Repeat, TRPV Cation Channels chemistry, TRPV Cation Channels genetics
Abstract

TRPV channels are important polymodal integrators of noxious stimuli mediating thermosensation and nociception. An ankyrin repeat domain (ARD), which is a common protein-protein recognition domain, is conserved in the N-terminal intracellular domain of all TRPV channels and predicted to contain three to four ankyrin repeats. Here we report the first structure from the TRPV channel subfamily, a 1.7 A resolution crystal structure of the human TRPV2 ARD. Our crystal structure reveals a six ankyrin repeat stack with multiple insertions in each repeat generating several unique features compared with a canonical ARD. The surface typically used for ligand recognition, the ankyrin groove, contains extended loops with an exposed hydrophobic patch and a prominent kink resulting from a large rotational shift of the last two repeats. The TRPV2 ARD provides the first structural insight into a domain that coordinates nociceptive sensory transduction and is likely to be a prototype for other TRPV channel ARDs.

Published
2006
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28. Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution.

Author

Xu Q, Schwarzenbacher R, Krishna SS, McMullan D, Agarwalla S, Quijano K, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Elsliger MA, Grittini C, Grzechnik SK, DiDonato M, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Miller MD, Moy K, Nigoghossian E, Paulsen J, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Animals, Binding Sites, Crystallization, Databases, Protein, Dioxygenases genetics, Dioxygenases metabolism, Metals chemistry, Mice, Models, Molecular, Molecular Sequence Data, Molecular Structure, Protein Binding, Protein Structure, Secondary, Protein Structure, Tertiary, Dioxygenases chemistry
Published
2006
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29. Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution.

Author

Mathews II, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Quaternary, Protein Structure, Tertiary, Structural Homology, Protein, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor chemistry, Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor metabolism, Thermotoga maritima enzymology
Published
2006
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30. Crystal structure of TM1367 from Thermotoga maritima at 1.90 A resolution reveals an atypical member of the cyclophilin (peptidylprolyl isomerase) fold.

Author

Jin KK, Krishna SS, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Feuerhelm J, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife C, Stevens RC, Spraggon G, van den Bedem H, Velasquez J, White A, Wolf G, Han GW, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins genetics, Binding Sites, Crystallography, X-Ray, Humans, Models, Molecular, Molecular Sequence Data, Peptidylprolyl Isomerase classification, Polyethylene Glycols, Protein Folding, Protein Structure, Quaternary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Bacterial Proteins metabolism, Cyclophilins chemistry, Cyclophilins metabolism, Peptidylprolyl Isomerase chemistry, Peptidylprolyl Isomerase metabolism, Thermotoga maritima enzymology
Published
2006
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31. Crystal structure of a single-stranded DNA-binding protein (TM0604) from Thermotoga maritima at 2.60 A resolution.

Author

DiDonato M, Krishna SS, Schwarzenbacher R, McMullan D, Jaroszewski L, Miller MD, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Chiu HJ, Deacon AM, Elsliger MA, Feuerhelm J, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Lesley SA, Moy K, Nigoghossian E, Okach L, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Anisotropy, Crystallography, X-Ray, DNA, Single-Stranded, Escherichia coli metabolism, Mitochondria metabolism, Models, Molecular, Molecular Sequence Data, Plasmids metabolism, Protein Structure, Secondary, Transcription Factors chemistry, X-Ray Diffraction, DNA-Binding Proteins chemistry, Thermotoga maritima metabolism
Published
2006
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32. Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold.

Author

Xu Q, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, White A, Wolf G, Hodgson KO, Wooley J, and Wilson IA

Subjects
Bacterial Proteins metabolism, Crystallography, X-Ray, Models, Molecular, Protein Folding, Protein Structure, Secondary, Virulence Factors metabolism, Bacterial Proteins chemistry, Campylobacter jejuni pathogenicity, Virulence Factors chemistry
Published
2006
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33. Crystal structure of a conserved hypothetical protein (gi: 13879369) from Mouse at 1.90 A resolution reveals a new fold.

Author

Klock HE, Schwarzenbacher R, Xu Q, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Koesema E, Kreusch A, Kuhn P, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Hodgson KO, Wooley J, Lesley SA, and Wilson IA

Subjects
Animals, Conserved Sequence, Crystallography, X-Ray, Mice, Models, Molecular, Molecular Weight, Open Reading Frames, Protein Folding, Protein Structure, Secondary, Databases, Protein, Proteins chemistry
Published
2005
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34. Crystal structure of Hsp33 chaperone (TM1394) from Thermotoga maritima at 2.20 A resolution.

Author

Jaroszewski L, Schwarzenbacher R, McMullan D, Abdubek P, Agarwalla S, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallization, Molecular Sequence Data, Zinc Fingers, Bacterial Proteins chemistry, Heat-Shock Proteins chemistry, Molecular Chaperones chemistry, Thermotoga maritima chemistry
Published
2005
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35. Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold.

Author

Rife C, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Dimerization, Molecular Sequence Data, Protein Folding, Bacterial Proteins chemistry, Models, Molecular, Pseudomonas putida, RNA-Binding Proteins chemistry
Published
2005
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36. Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 A resolution reveals a new fold.

Author

Rife C, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, DNA Gyrase metabolism, Dimerization, Molecular Sequence Data, Protein Folding, Bacterial Proteins chemistry, Models, Molecular, Thermotoga maritima enzymology
Published
2005
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37. Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution.

Author

Han GW, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Moy K, Nigoghossian E, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Animals, Crystallography, X-Ray, Mice, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Sensitivity and Specificity, Apoenzymes chemistry, Endoribonucleases chemistry, RNA, Messenger metabolism
Published
2005
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38. Crystal structure of S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA) from Thermotoga maritima at 2.0 A resolution reveals a new fold.

Author

Mathews I, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Axelrod H, Biorac T, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Moy K, Nigoghossian E, Ouyang J, Paulsen J, Quijano K, Reyes R, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Crystallography, X-Ray methods, Isomerases metabolism, Ligands, Models, Molecular, Protein Conformation, Solvents, Isomerases chemistry, Protein Folding, Thermotoga maritima enzymology
Published
2005
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39. Crystal structure of an indigoidine synthase A (IndA)-like protein (TM1464) from Thermotoga maritima at 1.90 A resolution reveals a new fold.

Author

Levin I, Miller MD, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Cambell J, Canaves JM, Chiu HJ, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Morse A, Moy K, Nigoghossian E, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA

Subjects
Bacterial Proteins metabolism, Crystallography, X-Ray, Models, Molecular, Piperidones metabolism, Protein Conformation, Protein Folding, Bacterial Proteins chemistry, Thermotoga maritima enzymology
Published
2005
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40. Crystal structure of a formiminotetrahydrofolate cyclodeaminase (TM1560) from Thermotoga maritima at 2.80 A resolution reveals a new fold.

Author

Xu Q, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hampton E, Hornsby M, Jaroszewski L, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Crystallization, Crystallography, X-Ray, Enzyme Stability, Models, Chemical, Models, Molecular, Molecular Conformation, Molecular Sequence Data, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Ammonia-Lyases chemistry, Thermotoga maritima enzymology
Published
2005
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41. Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor.

Author

Han GW, Schwarzenbacher R, Page R, Jaroszewski L, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nigoghossian E, Ouyang J, Paulsen J, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Electrons, Humans, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Stereoisomerism, Anabaena enzymology, Proteins chemistry, Transaminases chemistry
Published
2005
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42. Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution.

Author

Arndt JW, Schwarzenbacher R, Page R, Abdubek P, Ambing E, Biorac T, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Hornsby M, Klock HE, Koesema E, Kreusch A, Kuhn P, Jaroszewski L, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nigoghossian E, Ouyang J, Peti WS, Quijano K, Reyes R, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, White A, Wolf G, Xu Q, Zagnitko O, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Computational Biology, Models, Molecular, Molecular Conformation, Molecular Sequence Data, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Software, Crystallography, X-Ray methods, Hydrolases chemistry, Saccharomyces cerevisiae metabolism, Saccharomyces cerevisiae Proteins chemistry, Serine chemistry
Published
2005
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43. Methods and results for semi-automated cloning using integrated robotics.

Author

Klock HE, White A, Koesema E, and Lesley SA

Subjects
Genetic Vectors genetics, Oligonucleotides, Sequence Analysis, DNA, Cloning, Molecular methods, Genomics methods, Robotics instrumentation, Robotics methods
Abstract

The Joint Center for Structural Genomics (JCSG) has emphasized automation and parallel processing approaches. Here, we describe automated methods used across the cloning process with results from JCSG projects. The protocols for PCR, restriction digests and ligations, as well as for gel electrophoresis and microtiter plate assays have all been automated. The system has the capacity to routinely process 384 clones a week. This throughput can adequately supply our expression and purification pipeline with expression-ready clones, including novel targets and truncations. The utility of our system is demonstrated by our results from three diverse projects. In summary, 94% of the PCR amplicons generated to date have been successfully cloned and verified by sequencing (83% of the total attempted targets). Our results demonstrate the capabilities of this robotic platform to provide an avenue to high-throughput cloning which requires little manpower and is rapid and cost-effective while providing insights for method optimization.

Published
2005
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44. Crystal structure of a tandem cystathionine-beta-synthase (CBS) domain protein (TM0935) from Thermotoga maritima at 1.87 A resolution.

Author

Miller MD, Schwarzenbacher R, von Delft F, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Cambell J, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Cystathionine beta-Synthase chemistry, Thermotoga maritima enzymology
Published
2004
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45. Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold.

Author

Bakolitsa C, Schwarzenbacher R, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, Protein Structure, Secondary, Sequence Homology, Structural Homology, Protein, Bacterial Proteins chemistry, Thermotoga maritima chemistry
Published
2004
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46. Crystal structure of a putative NADPH-dependent oxidoreductase (GI: 18204011) from mouse at 2.10 A resolution.

Author

Levin I, Schwarzenbacher R, McMullan D, Abdubek P, Ambing E, Biorac T, Cambell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Animals, Binding Sites, Crystallography, X-Ray, Mice, Models, Molecular, Molecular Sequence Data, NADP metabolism, Oxidoreductases metabolism, Protein Structure, Secondary, Protein Structure, Tertiary, Quinone Reductases chemistry, Structural Homology, Protein, Oxidoreductases chemistry
Published
2004
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47. Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution.

Author

Jaroszewski L, Schwarzenbacher R, von Delft F, McMullan D, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshagi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Levin I, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Quijano K, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Crystallization, Manganese analysis, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes, Oxidoreductases chemistry, Protein Structure, Secondary, Protein Structure, Tertiary, Structural Homology, Protein, Bacterial Proteins chemistry, Thermotoga maritima chemistry
Published
2004
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48. Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution.

Author

Xu Q, Schwarzenbacher R, Page R, Sims E, Abdubek P, Ambing E, Biorac T, Brinen LS, Cambell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Quijano K, Reyes R, Rezezadeh F, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Conserved Sequence, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Multienzyme Complexes, Protein Structure, Secondary, Protein Structure, Tertiary, Structural Homology, Protein, Saccharomyces cerevisiae enzymology, Ureohydrolases chemistry
Published
2004
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49. Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution.

Author

McMullan D, Schwarzenbacher R, Jaroszewski L, von Delft F, Klock HE, Vincent J, Quijano K, Abdubek P, Ambing E, Biorac T, Brinen LS, Canaves JM, Dai X, Deacon AM, DiDonato M, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Karlak C, Koesema E, Kreusch A, Kuhn P, Levin I, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Page R, Reyes R, Rezezadeh F, Robb A, Sims E, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, Wolf G, Xu Q, Hodgson KO, Wooley J, Lesley SA, and Wilson IA

Subjects
Amino Acid Sequence, Binding Sites, Conserved Sequence, Crystallization, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Structural Homology, Protein, Bacterial Proteins chemistry, Thermotoga maritima enzymology
Published
2004
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50. Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution.

Author

Heine A, Canaves JM, von Delft F, Brinen LS, Dai X, Deacon AM, Elsliger MA, Eshaghi S, Floyd R, Godzik A, Grittini C, Grzechnik SK, Guda C, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MA, Miller MD, Morse A, Moy K, Ouyang J, Page R, Robb A, Rodrigues K, Schwarzenbacher R, Selby TL, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, Wang X, West B, Wolf G, Hodgson KO, Wooley J, and Wilson IA

Subjects
Amino Acid Sequence, Bacterial Proteins metabolism, Binding Sites, Crystallography, X-Ray, Cysteine Synthase metabolism, Ligands, Models, Molecular, Molecular Sequence Data, Phosphates metabolism, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Bacterial Proteins chemistry, Cysteine Synthase chemistry, Thermotoga maritima enzymology
Published
2004
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