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The NMR solution structure and function of RPA3313: a putative ribosomal transport protein from Rhodopseudomonas palustris.
- Source :
-
Proteins [Proteins] 2017 Jan; Vol. 85 (1), pp. 93-102. Date of Electronic Publication: 2016 Nov 13. - Publication Year :
- 2017
-
Abstract
- Protein function elucidation often relies heavily on amino acid sequence analysis and other bioinformatics approaches. The reliance is extended to structure homology modeling for ligand docking and protein-protein interaction mapping. However, sequence analysis of RPA3313 exposes a large, unannotated class of hypothetical proteins mostly from the Rhizobiales order. In the absence of sequence and structure information, further functional elucidation of this class of proteins has been significantly hindered. A high quality NMR structure of RPA3313 reveals that the protein forms a novel split ββαβ fold with a conserved ligand binding pocket between the first β-strand and the N-terminus of the α-helix. Conserved residue analysis and protein-protein interaction prediction analyses reveal multiple protein binding sites and conserved functional residues. Results of a mass spectrometry proteomic analysis strongly point toward interaction with the ribosome and its subunits. The combined structural and proteomic analyses suggest that RPA3313 by itself or in a larger complex may assist in the transportation of substrates to or from the ribosome for further processing. Proteins 2016; 85:93-102. © 2016 Wiley Periodicals, Inc.<br /> (© 2016 Wiley Periodicals, Inc.)
- Subjects :
- Amino Acid Motifs
Amino Acid Sequence
Bacterial Proteins genetics
Bacterial Proteins metabolism
Binding Sites
Carrier Proteins genetics
Carrier Proteins metabolism
Cloning, Molecular
Conserved Sequence
Escherichia coli genetics
Escherichia coli metabolism
Gene Expression
Ligands
Nuclear Magnetic Resonance, Biomolecular
Protein Binding
Protein Conformation, alpha-Helical
Protein Conformation, beta-Strand
Protein Folding
Protein Structure, Tertiary
Recombinant Proteins chemistry
Recombinant Proteins genetics
Recombinant Proteins metabolism
Rhodopseudomonas genetics
Rhodopseudomonas metabolism
Ribosomal Proteins genetics
Ribosomal Proteins metabolism
Ribosomes metabolism
Sequence Alignment
Sequence Homology, Amino Acid
Structure-Activity Relationship
Bacterial Proteins chemistry
Carrier Proteins chemistry
Rhodopseudomonas chemistry
Ribosomal Proteins chemistry
Ribosomes chemistry
Subjects
Details
- Language :
- English
- ISSN :
- 1097-0134
- Volume :
- 85
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Proteins
- Publication Type :
- Academic Journal
- Accession number :
- 27802574
- Full Text :
- https://doi.org/10.1002/prot.25201