Search

The three-dimensional structure of recombinant thermophilic ribokinase from Thermus speсies 2.9 was determined at 2.4 A resolution using crystals, which were grown in microgravity by the counter-diffusion method. The X-ray diffraction data were collected at the SPring-8 synchrotron facility (Japan). An adenosine diphosphate molecule is located in the active site of the enzyme, and its environment is described. The three-dimensional structure of Thermus species 2.9 ribokinase is shown to be very similar to the structures of other enzymes of this family.

Two recombinant purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 encoded by genes TT_C1070 (TthPNPI) and TT_C0194 (TthPNPII) were purified and characterized. T...

The apo form of the double mutant of Wolinella succinogenes L-asparaginase (WAS) with V23Q and K24T substitutions in the flexible N-terminal loop (WASm), which exhibits an order of magnitude lower glutaminase activity compared to the wild-type enzyme, was crystallized in two modifications (sp. grs. P22121 and P21). The three-dimensional structure in two modifications was determined at 1.5 and 1.7 A resolution, respectively. The three-dimensional structures and the molecular packing modes of the enzyme in two crystal modifications (monoclinic, sp. gr. P21, and orthorhombic, sp. gr. P22121) are compared. Intermolecular contacts and solvent channels in both crystal lattices are described. The orthorhombic crystals have a closer packing compared to the monoclinic crystals and lower water content (36.95 and 44.53%, respectively). However, the active sites in both structures are solvent accessible.

The mutant form of Wolinella succinogenes L-asparaginase (WASm) contains two replacements, V23Q and K24T, in the N-terminal flexible loop, which restricts the active center. This form of the enzyme has an order of magnitude lower glutaminase activity compared to the original enzyme (WAS). The 3D structure of WASm has been determined for the apo-form and WASm complexes with L-aspartic and L-glutamic amino acids with a resolution of 1.70, 1.65, and 2.0 A, respectively. The amino acid residues of the N-terminal flexible loop are only partially localized on electron density maps. In the corresponding complexes, all active centers of the tetrameric enzyme molecules are fully occupied with aspartic and glutamic acids. Their environment has been described, and their location in the original and mutant enzyme coincides. The state of the active centers in the studied molecules has been considered. It has been shown that the active centers in all subunits of the WASm apo-enzyme and WASm/Glu complex are in open conformation, while those in three subunits of the WASm/Asp complex are closed and the conformation is open only in one subunit. The comparison of three-dimensional structures of the original and mutant enzyme complexes suggests that the decrease in glutaminase activity of WASm is caused by the increase in the flexibility of the residues in the N‑terminal loop, which complicates the formation of the catalytically active closed form of the active center after the binding to the less specific substrate (glutamine).

Crystals of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPATMt), which were grown using 2-methyl-2,4-pentanediol (MPD) or ammonium sulfate as the precipitant, belong to sp. grs. R32 and Р32, respectively. Crystals of the enzyme containing the ligand in the active site were obtained by the cocrystallization of the enzyme with functional substrates only in the presence of MPD (sp. gr. R32). In the presence of ammonium sulfate, the ligand was not bound in the active site, and the cocrystallization resulted only in crystals of the apo form (sp. gr. Р32). The crystal-packing patterns of the enzyme molecules and the structure of the apo form of РРАТMt in two crystal structures are compared in order to explain the binding patterns of the ligand in different crystal modifications. In the crystal modification P32, the molecules are more closely packed compared to the crystal modification R32, and intermolecular contacts restrict the access to the active site.

The crystal structure of bacterial oligopeptidase B from Serratia proteamaculans (SpOpB) in complex with a chloromethyl ketone inhibitor was determined at 2.2 Å resolution. SpOpB was crystallized in a closed (catalytically active) conformation. A single inhibitor molecule bound simultaneously to the catalytic residues S532 and H652 mimicked a tetrahedral intermediate of the catalytic reaction. A comparative analysis of the obtained structure and the structure of OpB from Trypanosoma brucei (TbOpB) in a closed conformation showed that in both enzymes, the stabilization of the D-loop (carrying the catalytic D) in a position favorable for the formation of a tetrahedral complex occurs due to interaction with the neighboring loop from the β-propeller. However, the modes of interdomain interactions were significantly different for bacterial and protozoan OpBs. Instead of a salt bridge (as in TbOpB), in SpOpB, a pair of polar residues following the catalytic D617 and a pair of neighboring arginine residues from the β-propeller domain formed complementary oppositely charged surfaces. Bioinformatics analysis and structural modeling show that all bacterial OpBs can be divided into two large groups according to these two modes of D-loop stabilization in closed conformations.

Crystals of mutant carboxypeptidase T from Thermoactinomyces vulgaris (CPT11QG)with amino acid substitutions L211Q, T262S, L254S, and A251S were grown by the hanging-drop vapor-diffusion method. The crystals belong to sp. gr. P6(3)22. The X-ray-diffraction-data set,suitable for the crystal-structure determination at 2.6 A resolution,was collected from the grown crystals at the ID23-1 beamline of the European Synchrotron Radiation Facility (ESRF, France).

Crystals of mutant carboxypeptidase T from Thermoactinomyces vulgaris (CPT11QG) with amino-acid substitutions G215S, Q249G, A251G, T257A, D260G, T262D, and L254I and with the insertion ins253T were grown in microgravity by the capillary counter-diffusion method. The crystals belong to sp. gr. P31, which differs from the space group of the wild-type enzyme (P6322). The X-ray diffraction data set was collected from the crystals at the SPring-8 synchrotron facility (Japan) and is suitable for crystal structure determination at 2.45 A resolution.

The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl

The double mutant of Wolinella succinogenes L-asparaginase (Was72) with the V23Q and K24T substitutions in the C-terminal region of the N-terminal loop enclosing the active site was crystallized in the apo form and in complexes with L-aspartic and L-glutamic acids. This mutant exhibits glutaminase activity eight times lower compared to the wild-type enzyme. Crystals of the apo enzyme were grown in two modifications (sp. gr. P21 and sp. gr. P22121). Crystals grown in the presence of both aspartic and glutamic acids belong to the same space group (P21) but have different unit cell parameters. The X-ray diffraction data sets were collected from all types of crystals at 1.65–2.00 A resolution. All X-ray diffraction data sets are suitable for the determination of the three-dimensional structure of the enzyme.

A mutant of bacterial carboxypeptidase T from Thermoactinomyces vulgaris (CPT5) with amino-acid substitutions in the S1' specificity pocket of the active site for the residues corresponding to the S1' region of pancreatic carboxypeptidase B (Gly215Ser, Ala251Gly, Thr257Ala, Asp260Gly, Thr262Asp) was crystallized in complex with N-BOC-L-Leu. The latter occupies the S1 subsite of the active site and is a reaction product analog. The X-ray diffraction data set was collected from a crystal of CPT5 at the SPring 8 synchrotron facility. The three-dimensional structure of CPT5 was determined at 1.40 A resolution and refined to Rfact = 13.6%, Rfree = 12.5%. The binding of N-BOC-L-Leu to the S1 subsite of CPT5 leads to conformational changes in the protein concerning primarily the Сα atoms of five residues of the flexible loop at the interface between the S1 and S1' subsites and the side chains of the residues Tyr255 and Leu254 involved in the induced fit. Besides, conformational changes are observed in the active-site residues Glu277 and Asp262 and the side chains of residues located on the surface of the protein molecule. The observed changes differ from the conformational changes, which occur upon binding of N-BOC-L-Leu to wild-type CPT. This fact is indicative of the mutual influence of the S1 and S1' subsites in metallocarboxypeptidase T.

The positions of the substrates (ATP and ribose 5 phosphate) of phosphoribosylpyrophosphate synthetase from Thermus thermophilus were determined by molecular dynamics simulations. The simulation brought the system to an equilibrium state, with the binding poses of the ligands in the active site being stable. Based on the results of simulation of the complex, the environment of the substrates was analyzed and the amino-acid residues of the enzyme that form polar interactions with the substrates were identified. Candidate sites for mutagenesis, which can be mutated in order to broaden the substrate specificity toward ribose 5-phosphate, are proposed.

Models of E. coli thymidine phosphorylase in complexes with the substrates — the complex with phosphate and the complex with phosphate and thymidine — were obtained by molecular docking calculations. The influence of the substrates on domain movements in the dimeric thymidine phosphorylase molecule was probed by molecular dynamics simulations. The two subunits were shown to function asynchronously. In the thymidine phosphorylase/phosphate and thymidine phosphorylase/phosphate/thymidine complexes, phosphate is more weakly bound in the active site and moves away from the phosphate-binding site during the 60-ns trajectory, whereas thymidine remains in the active site but undergoes conformational changes.

Two recombinant purine nucleoside phosphorylases from thermophilic bacterium

It is generally accepted that the primary specificity of metallocarboxypeptidases is mainly determined by the structure of the so-called primary specificity pocket. However, the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT) with the primary specificity pocket fully reproducing the one in pancreatic carboxypeptidase B (CPB) retained the broad, mainly hydrophobic substrate specificity of the wild-type enzyme. In order to elucidate factors affecting substrate specificity of metallocarboxypeptidases and the reasons for the discrepancy with the established views, we have solved the structure of the complex of the CPT G215S/A251G/T257A/D260G/T262D mutant with the transition state analogue N-sulfamoyl-L-phenylalanine at a resolution of 1.35 Å and compared it with the structure of similar complex formed by CPB. The comparative study revealed a previously underestimated structural determinant of the substrate specificity of metallocarboxypeptidases and showed that even if substitution of five amino acid residues in the primary specificity pocket results in its almost complete structural correspondence to the analogous pocket in CPB, this does not lead to fundamental changes in the substrate specificity of the mutant enzyme due to the differences in the structure of the mobile loop located at the active site entrance that affects the substrate-induced conformational rearrangements of the active site.

Adenine phosphoribosyltransferase (APRT) from a thermophilic bacterial strain Thermus thermophilus НВ27 (TthHB27APRT) belongs to the family of type I phosphoribosyltransferases and catalyzes the magnesium-dependent transfer of 5'-phosphoribosyl group from 5'-phosphoribosylpyrophosphate to N9 adenine nitrogen with formation of adenosine-5'-monophosphate and pyrophosphate. The crystals of the recombinant enzyme suitable for X-ray study were grown in a capillary using the counter-diffusion technique. Crystals with unit-cell parameters α = 69.860 A, b = 82.160 A, c = 91.390 A, α = 90.00°, β = 102.58°, and γ = 90.00° belong to the space group Р21 and contain six enzyme monomers in the asymmetric unit. The set of X-ray data from grown crystals was collected on a Spring-8 synchrotron radiation facility (Japan) and three-dimensional structure of the enzyme was solved at 2.7-A resolution by molecular replacement method using the BALBES software. The polypeptide fold in the enzyme monomer and the structure of biologically active dimer were described. Based on the comparison with structures of homologous APRTs from a thermophilic strain ThtHB8 and Homo sapiens, positions of active site and a number of functionally important amino acids were located.

Bacterial imidazoleglycerol-phosphate dehydratase from Mycobacterium tuberculosis (HisB-Mt) is a convenient target for the discovery of selective inhibitors as potential antituberculosis drugs. The virtual screening was performed to find compounds suitable for the design of selective inhibitors of HisB-Mt. The positions of four ligands, which were selected based on the docking scoring function and docked to the activesite region of the enzyme, were refined by molecular dynamics simulation. The nearest environment of the ligands was determined. These compounds selectively bind to functionally essential active-site residues, thus blocking access of substrates to the active site of the enzyme, and can be used as lead compounds for the design of selective inhibitors of HisB-M.

Carboxypeptidase T (CPT, EC 3.4.17.18) from Thermoactinomyces vulgaris is a distant homolog of the highly specific pancreatic carboxypeptidase B, but has a broad substrate specificity, the source of which remains unclear. A previous study of the structural bases of the substrate specificity of CPT using stable sulfamoyl analogs of the transition state of the elimination of leucine, phenylalanine, arginine, and glutamic acid, showed that the binding of the C-terminal residue of the substrate to the primary selectivity pocket of CPT leads to a change in the distance between Zn2+ and the sulfur atom. This value is related to the efficiency of catalysis of the corresponding substrate or the inhibition constant of the corresponding stable analog of the transition state. In this work, we obtained crystallographic and kinetic data of the complex of CPT with N-sulfamoyl-L-valine, confirming the effect of the binding of the ligand’s side group by the primary specificity pocket of CPT on the structure of the catalytic center, which can explain the unusual substrate specificity of CPT.

Metallocarboxypeptidases (MCPs) have been in a focus of biochemical studies since 1954 when carboxypeptidase A (CPA) was discovered as the second, after carbonic anhydrase, zinc-dependent enzyme up...

Adenine phosphoribosyltransferase (APRT) belongs to the type I phosphoribosyltransferase family and catalyzes the formation of adenosine monophosphate via transfer of the 5-phosphoribosyl group from phosphoribosyl pyrophosphate to the nitrogen atom N9 of the adenine base. Proteins of this family are involved in a salvage pathway of nucleotide synthesis, thus providing purine base utilization and maintaining the optimal level of purine bases in the body. Adenine phosphoribosyltransferase from the extremely thermophilic Thermus thermophilus strain HB27 was produced using a highly efficient E. coli producer strain and was then purified by affinity and gel-filtration chromatography. This enzyme was successfully employed as a catalyst for the cascade biosynthesis of biologically important nucleotides. The screening of crystallization conditions for recombinant APRT from T. thermophilus HB27 was performed in order to determine the enzyme structure by X-ray diffraction. The crystallization conditions, which were found by the vapor-diffusion technique, were then optimized to apply the counter-diffusion technique. The crystals of the enzyme were grown by the capillary counter-diffusion method. The crystals belong to sp. gr. P1211 and have the following unitcell parameters: a = 69.86 A, b = 82.16 A, c = 91.39 A, α = γ = 90°, β = 102.58°. The X-ray diffraction data set suitable for the determination of the APRT structure at 2.6 A resolution was collected from the crystals at the SPring-8 synchrotron facility (Japan).

Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strainThermus thermophilusHB27 catalyzes the synthesis of phosphoribosylpyrophosphate from ribose 5-phosphate and ATP, and belongs to the class I PRPPSs. The three-dimensional structure of the recombinant enzyme was solved at 2.2 Å resolution using crystals grown in microgravity from protein solution containing ATP, magnesium and sulfate ions. An ADP molecule was located in the active site of each subunit of the hexameric enzyme molecule and sulfate ions were located in both the active and allosteric sites. It was found that the catalytic loop that restricts the active-site area and is usually missing from the electron-density map of class I PRPPSs adopts different conformations in three independent subunits inT. thermophilusPRPPS. A closed conformation of the active site was found in one of subunits where the highly ordered catalytic β-hairpin delivers the Lys and Arg residues that are essential for activity directly to the ADP molecule, which occupies the ATP-binding site. A comparison of the conformations of the catalytic loop in the three independent subunits reveals a possible mode of transition from the open to the closed state of the active site during the course of the catalyzed reaction.

Bacterial phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPAT Mt) is a convenient target protein for the directed search for selective inhibitors as potent antituberculosis drugs. Four compounds suitable for the detailed investigation of their interactions with PPAT Mt were found by virtual screening. The active-site region of the enzyme was chosen as the ligand-binding site. The positions of the ligands found by the docking were refined by molecular dynamics simulation. The nearest environment of the ligands, the positions of which in the active site of the enzyme were found in a computational experiment, was analyzed. The compounds under consideration were shown to directly interact with functionally important active-site amino-acid residues and block access of substrates to the active site. Therefore, these compounds can be used for the design of selective inhibitors of PPAT Mt as potent antituberculosis drugs.

Crystals of porcine pancreatic carboxypeptidase B (CPB) were grown by the capillary counter-diffusion method in the presence of polyethylene glycol and zinc acetate. The three-dimensional structure of CPB was determined at 1.40 A resolution using the X-ray diffraction data set collected from the crystals of the enzyme at the SPring 8 synchrotron facility and was refined to Rfact = 17.19%, Rfree = 19.78%. The structure contains five zinc atoms, two of which are present in the active site of the enzyme, and an acetate ion. The arrangement of an additional zinc atom in the active site and the acetate ion is different from that reported by Yoshimoto et al.

Phosphoribosylpyrophosphate synthetases (PRPP synthetases) are among the key enzymes essential for vital functions of organisms and are involved in the biosynthesis of purine and pyrimidine nucleotides, coenzymes, and the amino acids histidine and tryptophan. These enzymes are used in biotechnology for the combined chemoenzymatic synthesis of natural nucleotide analogs. Recombinant phosphoribosylpyrophosphate synthetase I from the thermophilic strain HB27 of the bacterium Thermus thermophilus (T. th HB27) has high thermal stability and shows maximum activity at 75°С, due to which this enzyme holds promise for biotechnological applications. In order to grow crystals and study them by X-ray crystallography, an enzyme sample, which was produced using a highly efficient producer strain, was purified by affinity and gel-filtration chromatography. The screening of crystallization conditions was performed by the vapor-diffusion technique. The crystals of the enzyme suitable for X-ray diffraction were grown by the counter-diffusion method through a gel layer. These crystals were used to collect the X-ray diffraction data set at the SPring-8 synchrotron radiation facility (Japan) to 3-A resolution. The crystals belong to sp. gr. P21 and have the following unitcell parameters: a = 107.7 A, b = 112.6 A, c = 110.2 A, α = γ = 90°, β = 116.6°. The X-ray diffraction data set is suitable for determining the three-dimensional structure of the enzyme at 3.0-A resolution.

Carboxypeptidase T (CPT) from Thermoactinomyces vulgaris (EC 3.4.17.18) has a broad substrate specificity, the mechanism of which remains unclear. It cleaves off arginine residues by 10, and lysine residues by 100 times worse than hydrophobic leucine residues despite the presence of negatively charged Asp260 at the bottom of the primary specificity pocket. To study the relationship between the structure and specificity the 3D structure of CPT in complex with the stable transition state analog N-sulfamoyl-l-lysine (SLys) was determined in which the S-atom imitates the sp3-hybridized carbon in the scissile-bond. Crystals grown in microgravity has the symmetry of space group P6322. The present complex structure was compared with the previously reported complex structure of CPT and N-sulfamoyl-L-arginine (SArg). The location/binding of SLys in the active site of CPT very closely resembled that of SArg, and the positively charged N-atom of SLys was at the same position as the corresponding positively charged N-atom of SArg. The SLys complex is stabilized by the hydrogen bond between the nitrogen atom and OH-group of Thr257. The contact areas of the residues Tyr255, Leu211, and Thr262 with SLys were reduced in comparison with the same of SArg. This difference in bonding of SArg and SLys side chains in the primary specificity pocket induces shifts differences within the catalytic center (especially Tyr255-O20 and S18-Arg129 N1 gap) that may influence the enzyme's catalytic reaction. Therefore, this information may be useful for the design of carboxypeptidases with improved selectivity towards Arg/Lys for biotechnological applications.

Two genes of T. thermophilus HB27, TT_C1184 and TT_C1274, encoding proteins with phosphoribosyl pyrophosphate synthetase activity were cloned in an expressing vector pET23d+. Escherichia coli strains overproducing two relevant proteins in soluble forms were obtained. The methods of isolation of thermophilic phosphoribosyl pyrophosphate synthetases Tth PRPPS1 and Tth PRPPS2 were developed. The activities of these enzymes were determined as a function of concentration of metal ions, inorganic phosphate, and temperature. The kinetic parameters for basic natural substrates were calculated; the substrate specificity for different carbohydrate 5-phosphates of D-series was studied. It was shown that the two proteins differ significantly in these characteristics. According to the results and comparison of amino acid sequences of new proteins with those of other phosphoribosyl pyrophosphate synthetases, both enzymes belong to class I PRPPS.

Conditions of mass transport to growing crystals have a considerable effect on the crystal size and quality. The reduction of convective transport can help improve the quality of crystals for X-ray crystallography. One approach to minimizing convective transport is crystallization in a microgravity environment, in particular, in space. The data obtained by our research team in protein crystallization experiments on the International Space Station are surveyed and analyzed.

Purine nucleoside phosphorylases (PNPs) catalyze the reversible phosphorolysis of nucleosides and are key enzymes involved in nucleotide metabolism. They are essential for normal cell function and can catalyze the transglycosylation. Crystals of E. coli PNP were grown in microgravity by the capillary counterdiffusion method through a gel layer. The three-dimensional structure of the enzyme was determined by the molecular-replacement method at 0.99 A resolution. The structural features are considered, and the structure of E. coli PNP is compared with the structures of the free enzyme and its complexes with purine base derivatives established earlier. A comparison of the environment of the purine base in the complex of PNP with formycin A and of the pyrimidine base in the complex of uridine phosphorylase with thymidine revealed the main structural features of the base-binding sites. Coordinates of the atomic model determined with high accuracy were deposited in the Protein Data Bank (PDB_ID: 4RJ2).

Phosphoribosyl pyrophosphate synthetase from Escherichia coli was cloned, purified, and crystallized. Single crystals of the enzyme were grown under microgravity. The X-ray diffraction data set was collected at the Spring-8 synchrotron facility and used to determine the three-dimensional structure of the enzyme by the molecular-replacement method at 2.71 A resolution. The active and regulatory sites in the molecule of E. coli phosphoribosyl pyrophosphate synthetase were revealed by comparison with the homologous protein from Bacillus subtilis, the structure of which was determined in a complex with functional ligands. The conformations of polypeptide-chain fragments surrounding and composing the active and regulatory sites were shown to be identical in both proteins.

A site-directed mutagenesis method has been used to obtain the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT), in which the amino-acid residues of the S1′ subsite are substituted by the corresponding residues from pancreatic carboxypeptidase B (CPB). It was shown that the mutant enzyme retained the broad, mainly hydrophobic selectivity of wild-type CPT. The mutant containing the implanted CPB S1′ subsite was crystallized and its three-dimensional structure was determined at 1.29 Å resolution by X-ray crystallography. A comparison of the three-dimensional structures of CPT, the G215S/A251G/T257A/D260G/T262D CPT mutant and CPB showed that the S1′ subsite of CPT has not been distorted by the mutagenesis and adequately reproduces the structure of the CPB S1′ subsite. The CPB-like mutant differs from CPB in substrate selectivity owing to differences between the two enzymes outside the S1′ subsite. Moreover, the difference in substrate specificity between the enzymes was shown to be affected by residues other than those that directly contact the substrate.

Purine nucleoside phosphorylases (EC 2.4.2.1; PNPs) reversibly catalyze the phosphorolytic cleavage of glycosidic bonds in purine nucleosides to generate ribose 1-phosphate and a free purine base, and are key enzymes in the salvage pathway of purine biosynthesis. They also catalyze the transfer of pentosyl groups between purine bases (the transglycosylation reaction) and are widely used for the synthesis of biologically important analogues of natural nucleosides, including a number of anticancer and antiviral drugs. Potent inhibitors of PNPs are used in chemotherapeutic applications. The detailed study of the binding of purine bases and their derivatives in the active site of PNPs is of particular interest in order to understand the mechanism of enzyme action and for the development of new enzyme inhibitors. Here, it is shown that 7-deazahypoxanthine (7DHX) is a noncompetitive inhibitor of the phosphorolysis of inosine by recombinantEscherichia coliPNP (EcPNP) with an inhibition constantKiof 0.13 mM. A crystal ofEcPNP in complex with 7DHX was obtained in microgravity by the counter-diffusion technique and the three-dimensional structure of theEcPNP–7DHX complex was solved by molecular replacement at 2.51 Å resolution using an X-ray data set collected at the SPring-8 synchrotron-radiation facility, Japan. The crystals belonged to space groupP6122, with unit-cell parametersa=b= 120.370,c= 238.971 Å, and contained three subunits of the hexameric enzyme molecule in the asymmetric unit. The 7DHX molecule was located with full occupancy in the active site of each of the three crystallographically independent enzyme subunits. The position of 7DHX overlapped with the positions occupied by purine bases in similar PNP complexes. However, the orientation of the 7DHX molecule differs from those of other bases: it is rotated by ∼180° relative to other bases. The peculiarities of the arrangement of 7DHX in theEcPNP active site are discussed.

Enzymes of the phosphoribosyl pyrophosphate synthetase family (PRPPS, EC 2.7.6.1) catalyze the formation of 5-phosphoribosyl pyrophosphate (5-PRPP) from adenosine triphosphate and ribose 5-phosphate. 5-Phosphoribosyl pyrophosphate is an important intermediate in the synthesis of purine, pyrimidine, and pyridine nucleotides, as well as of the amino acids histidine and tryptophan. The crystallization conditions for E. coli PRPPS were found by the vapor-diffusion technique and were optimized to apply the capillary counter-diffusion technique. The X-ray diffraction data set was collected from the crystals grown by the counter-diffusion technique using a synchrotron radiation source to 3.1-A resolution. The crystals of PRPPS belong to sp. gr. P6322 and have the following unit-cell parameters: a = b = 104.44 A, c = 124.98 A, α = β = 90°, γ = 120°. The collected X-ray diffraction data set is suitable for the solution of the three-dimensional structure of PRPPS at 3.1-A resolution.

Crystals of E. coli purine nucleoside phosphorylase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 0.99 A resolution. The crystals belong to sp. gr. P21 and have the following unit-cell parameters: a = 74.1 A, b = 110.2 A, c = 88.2 A, α = γ = 90°, β = 111.08°. The crystal contains six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is the biological active form of E. coli. purine nucleoside phosphorylase.

The crystal structures of carboxypeptidase T (CpT) complexes with phenylalanine and arginine substrate analogs - benzylsuccinic acid and (2-guanidinoethylmercapto)succinic acid - were determined by the molecular replacement method at resolutions of 1.57 Å and 1.62 Å to clarify the broad substrate specificity profile of the enzyme. The conservative Leu211 and Leu254 residues (also present in both carboxypeptidase A and carboxypeptidase B) were shown to be structural determinants for recognition of hydrophobic substrates, whereas Asp263 was for recognition of positively charged substrates. Mutations of these determinants modify the substrate profile: the CpT variant Leu211Gln acquires carboxypeptidase B-like properties, and the CpT variant Asp263Asn the carboxypeptidase A-like selectivity. The Pro248-Asp258 loop interacting with Leu254 and Tyr255 was shown to be responsible for recognition of the substrate's C-terminal residue. Substrate binding at the S1' subsite leads to the ligand-dependent shift of this loop, and Leu254 side chain movement induces the conformation rearrangement of the Glu277 residue crucial for catalysis. This is a novel insight into the substrate selectivity of metallocarboxypeptidases that demonstrates the importance of interactions between the S1' subsite and the catalytic center.

The crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding module (CBM) from laminarinase Lic16A of the hyperthermophilic anaerobic bacteriumClostridium thermocellum(ctCBM54) are reported. Recombinant ctCBM54 was prepared using anEscherichia coli/pQE30 overexpression system and was crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.1 Å resolution using synchrotron radiation. The crystals belonged to space groupP6322, with unit-cell parametersa=b= 130.15,c= 131.05 Å. The three-dimensional structure of ctCBM54 will provide valuable information about the structure–function relation of the laminarinase Lic16A and will allow the exploitation of this binding module in biotechnological applications.

Carboxypeptidase B (EC 3.4.17.2) (CPB) is commonly used in the industrial insulin production and as a template for drug design. However, its ability to discriminate substrates with hydrophobic, hydrophilic, and charged side chains is not well understood. We report structure of CPB complex with a transition state analog N-sulfamoyl-L-phenylalanine solved at 1.74Å. The study provided an insight into structural basis of CPB substrate specificity. Ligand binding is affected by structure-depended conformational changes of Asp255 in S1'-subsite, interactions with Asn144 and Arg145 in C-terminal binding subsite, and Glu270 in the catalytic center. Side chain of the non-specific substrate analog SPhe in comparison with that of specific substrate analog SArg (reported earlier) not only loses favorable electrostatic interactions and two hydrogen bonds with Asp255 and three fixed water molecules, but is forced to be in the unfavorable hydrophilic environment. Thus, Ser207, Gly253, Tyr248, and Asp255 residues play major role in the substrate recognition by S1'-subsite.

The results of studying crystallization in space are reviewed with focus on the growth of semiconductor and protein crystals. The history of the problem is considered, the influence of microgravity on the crystal growth is investigated, and the main experimental data on crystal growth in zero gravity are analyzed. The studies performed in this field at the Institute of Crystallography, Russian Academy of Sciences (IC RAS), are reviewed in detail.

The carboxypeptidase T (CPT) from Thermoactinomyces vulgaris has an active site structure and 3D organization similar to pancreatic carboxypeptidases A and B (CPA and CPB), but differs in broader substrate specificity. The crystal structures of CPT complexes with the transition state analogs N-sulfamoyl-L-leucine and N-sulfamoyl-L-glutamate (SLeu and SGlu) were determined and compared with previously determined structures of CPT complexes with N-sulfamoyl-L-arginine and N-sulfamoyl-L-phenylalanine (SArg and SPhe). The conformations of residues Tyr255 and Glu270, the distances between these residues and the corresponding ligand groups, and the Zn-S gap between the zinc ion and the sulfur atom in the ligand’s sulfamoyl group that simulates a distance between the zinc ion and the tetrahedral sp3-hybridized carbon atom of the converted peptide bond, vary depending on the nature of the side chain in the substrate’s C-terminus. The increasing affinity of CPT with the transition state analogs in the order SGlu, SArg, SPhe, SLeu correlates well with a decreasing Zn-S gap in these complexes and the increasing efficiency of CPT-catalyzed hydrolysis of the corresponding tripeptide substrates (ZAAL > ZAAF > ZAAR > ZAAE). Thus, the side chain of the ligand that interacts with the primary specificity pocket of CPT, determines the geometry of the transition complex, the relative orientation of the bond to be cleaved by the catalytic groups of the active site and the catalytic properties of the enzyme. In the case of CPB, the relative orientation of the catalytic amino acid residues, as well as the distance between Glu270 and SArg/SPhe, is much less dependent on the nature of the corresponding side chain of the substrate. The influence of the nature of the substrate side chain on the structural organization of the transition state determines catalytic activity and broad substrate specificity of the carboxypeptidase T.

Crystals of M. tuberculosis phosphopantetheine adenylyltransferase were grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one crystal at the Spring-8 synchrotron facility to 2.00-A resolution. The crystals belong to sp. gr. P32 and have the following unit-cell parameters: a = b = 106.47 A, c = 71.32 A, α = γ = 90°, β = 120°. The structure was solved by the molecular-replacement method. There are six subunits of the enzyme comprising a hexamer per asymmetric unit. The hexamer is a biologically active form of phosphopantetheine adenylyltransferase from M. tuberculosis.

Crystals of porcine pancreatic carboxypeptidase B have been grown in microgravity by the capillary counter-diffusion method through a gel layer. The X-ray diffraction study showed that the crystals belong to sp. gr. P41212 and have the following unit-cell parameters: a = b = 79.58 A, c = 100.51 A; α = β = γ = 90.00°. The X-ray diffraction data set suitable for the determination of the three-dimensional structure at atomic resolution was collected from one of the grown crystals at the SPring 8 synchrotron facility to 0.98 A resolution.

The threedimensional structures of thymidine phosphorylase from E. coli containing the bound sulfate ion in the phosphatebinding site and of the co mplex of thymidine phosphorylase with sulfate in the phosphatebinding site and the inhibitor 3'�azido�2'�fluoro�2',3'�dideoxyuridine ( N3FddU ) in the nucleo� sidebinding site were determined at 1.55 and 1.50 A resolution, respectively. The aminoacid residues involved in the ligand binding and the hydrogenbond network in the active site occupied by a large number of bound water molecules are described. A comparison of the structure of thymidine phosphorylase in com� plex with N3 FddU with the structure of pyrimidine nucleoside phosphorylase from St. Aureus in complex with the natural substrate thymidine (PDB_ID: 3H5Q) shows that the substrate and the inhibitor in the nucleosidebinding pocket have different orientations. It is suggested that the position of N3FddU can be influenced by the presence of the azido group, which prefers a hydrophobic environment. In both structures, the active sites of the subunits are in the open conformation.

Structures of recombinant phosphopantetheine adenylyltransferase (PPAT) fromMycobacterium tuberculosis(PPATMt) in the apo form and in complex with the substrate ATP were determined at 1.62 and 1.70 Å resolution, respectively, using crystals grown in microgravity by the counter-diffusion method. The ATP molecule of the PPATMt–ATP complex was located with full occupancy in the active-site cavity. Comparison of the solved structures with previously determined structures of PPATMt complexed with the reaction product dephosphocoenzyme A (dPCoA) and the feedback inhibitor coenzyme A (CoA) was performed using superposition on Cαatoms. The peculiarities of the arrangement of the ligands in the active-site cavity of PPATMt are described. The conformational states of the PPAT molecule in the consequent steps of the catalyzed reaction in the apo enzyme and the enzyme–substrate and enzyme–product complexes are characterized. It is shown that the binding of ATP and dPCoA induces the rearrangement of a short part of the polypeptide chain restricting the active-site cavity in the subunits of the hexameric enzyme molecule. The changes in the quaternary structure caused by this rearrangement are accompanied by a variation of the size of the inner water-filled channel which crosses the PPAT molecule along the threefold axis of the hexamer. The molecular mechanism of the observed changes is described.

Crystals of phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium tuberculosis in the apo form and in complexes with coenzyme A (PPAT/CoA) and dephosphocoenzyme A (PPAT/dPCoA) were grown in microgravity by the capillary counter-diffusion method. The structures of PPAT Mt in the apo form and in complexes with ligands were solved based on the X-ray diffraction data collected from the grown crystals. The crystal structures were refined at 1.76, 1.59, and 1.59 A resolution to Rf factors of 0.175, 0.159, and 0.157 and Rfree of 0.224, 0.208, and 0.206 for PPAT, PPAT/CoA, and PPAT/dPCoA, respectively. The atomic coordinates of the structures were deposited in the Protein Data Bank (PDB ID: 3RFF, 3RHS, and 3RBA). In these structures, the ligand-binding sites were determined, the environment of these sites was characterized, and the conformational changes accompanying the ligand binding were analyzed.

Crystals of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis, thymidine phosphorylase from Escherichia coli, carboxypeptidase T from Thermoactinomyces vulgaris and its mutant forms, and crystals of complexes of these proteins with functional ligands and inhibitors were grown by the capillary counter-diffusion method in the Japanese Experimental Module Kibo on the International Space Station. The high-resolution X-ray diffraction data sets suitable for the determination of high-resolution three-dimensional structures of these proteins were collected from the grown crystals on the SPring-8 synchrotron radiation facility. The conditions of crystal growth for the proteins and the data-collection statistics are reported. The crystals grown in microgravity diffracted to a higher resolution than crystals of the same proteins grown on Earth.

Crystals of recombinant carboxypeptidase T (CPT) from Thermoactinomyces vulgaris were grown in a capillary by the counterdiffusion method in the absence of calcium ions. The three-dimensional structure of CPT was solved at 1.69-A resolution using the X-ray diffraction data collected from the crystals of the enzyme on the SPring-8 synchrotron radiation facility and was then refined to Rfact = 16.903% and Rfree = 18.165%. The coordinates of the refined model were deposited in the Protein Data Bank (PDB ID: 3QNV). A comparison of this structure with the structure of wild-type CPT containing bound calcium ions, which was determined earlier, revealed a number of conformational changes both in the calcium-binding sites and the enzyme active site. Based on the results of this comparison, the possible factors responsible for the difference in the catalytic activity of the two forms of the enzyme are considered.

Recombinant phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis (PPAT Mt), which was produced by a high-producing strain and purified to 99%, was used for the crystal growth of the complex of the enzyme with coenzyme A (CoA). Crystals suitable for X-ray diffraction study were obtained by cocrystallization. The crystals belong to sp. gr. R32 and have the unit-cell parameters a = b = 98.840 A, c = 112.880 A, α = β = 90.00°, and γ = 120.00°. The three-dimensional structure of the complex was determined based on X-ray diffraction data collected from the crystals to 2.1 A resolution and refined to Rf = 22.7% and Rfree = 25.93%. Active-site bound coenzyme A was found, and its nearest environment was described. The conformational changes of the enzyme due to ligand binding were revealed. The binding of CoA by tuberculosis phosphopantetheine adenylyltransferase was characterized by comparing the structures of the title complex to a similar complex of PPAT from E. coli (PPAT Ec).

Recombinant G215S, A251G, T257A, D260G, T262D mutant carboxypeptidase T from Thermoactinomyces vulgaris containing mutations in the primary specificity pocket was prepared and crystallized. Single crystals with a size of up to 0.3 mm were grown and investigated by X-ray diffraction. Recombinant mutant carboxypeptidase T containing the primary specificity subsite compositionally identical to that of pancreatic carboxypeptidase B crystallizes in the same space group as the natural enzyme. The crystals belong to sp. gr. P6322; the unit-cell parameters are a = b = 157.867 A, c = 104.304 A, α = β = 90°, γ = 120°. X-ray diffraction data suitable for determining the three-dimensional structure at atomic resolution were collected from one crystal.

Crystals of high-purity recombinant NAD+-dependent formate dehydrogenase from the higher plant Arabidopsis thaliana (AraFDH) were grown in microgravity in the Modul’-1 protein crystallization apparatus on the International Space Station. The space-grown crystals have larger sizes than those grown on Earth. X-ray diffraction data suitable for determining the three-dimensional structure were collected from the space-grown crystals to a resolution of 1.22 A using an X-ray synchrotron source. The crystals belong to sp. gr. P43212; the unit-cell parameters are a = b = 107.865 A, c = 71.180 A, α = β = γ = 90°.

Protealysin (PLN) belongs to the M4 family of peptidases that are commonly known as thermolysin-like proteases (TLPs). All TLPs are synthesized as precursors containing N-terminal propeptides. According to the primary structure of the N-terminal propeptides, the family is divided into two distinct groups. Representatives of the first group including thermolysin and all TLPs with known three-dimensional structures have long prosequences (∼200 amino acids). Enzymes of the second group, whose prototype is protealysin, have short (∼50 amino acids) propeptides. Here, we present the 1.8 A crystal structure of PLN precursor (proPLN), which is the first three-dimensional structure of a TLP precursor. Whereas the structure of the catalytic domain of proPLN is similar overall to previously reported structures of mature TLPs, it has specific features, including the absence of calcium-binding sites, and different structures of the N-terminal region and substrate-binding site. PLN propeptide forms a separate domain in the precursor and likely acts as an inhibitor that blocks the substrate-binding site and fixes the “open” conformation of the active site, which is unfavorable for catalysis. Furthermore the conserved PPL motif identified in our previous studies directly interacts with the S′ subsites of the active center being a critical element of the propeptide-catalytic domain interface. Comparison of the primary structures of TLPs with short propeptides suggests that the specific features revealed in the proPLN crystal structure are typical for all protealysin-like enzymes. Thus, such proteins can be considered as a separate subfamily of TLPs.

Experiments on protein crystallization on the Russian segment of the International Space Station were started in 2005. These experiments were performed in the Modul’-1 protein crystallization apparatus specially designed for crystal growth by the free-interface-diffusion method. This paper describes experiments on the crystallization of lysozyme, carboxypeptidase B, and recombinant human insulin on Earth and in microgravity using the Modul’-1 protein crystallization apparatus during the ISS-11-ISS-14 space flights. Crystals of all proteins grown in microgravity have larger sizes than those grown on Earth. Space-grown crystals of lysozyme and insulin characterized by X-ray diffraction were shown to diffract to higher resolution than the Earth-grown crystals. The three-dimensional structures of Zn-insulin crystals grown both on Earth and in microgravity were established. The conformation of the Zn-insulin hexamer in the crystalline state is described.