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Tran QD, Tran V, Toh LS, Williams PM, Tran NN, Hessel V. Space Medicines for Space Health. ACS Med Chem Lett 2022; 13:1231-1247. [PMID: 35978686 PMCID: PMC9377000 DOI: 10.1021/acsmedchemlett.1c00681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Scientists from around the world are studying the effects of microgravity and cosmic radiation via the "off-Earth" International Space Station (ISS) laboratory platform. The ISS has helped scientists make discoveries that go beyond the basic understanding of Earth. Over 300 medical experiments have been performed to date, with the goal of extending the knowledge gained for the benefit of humanity. This paper gives an overview of these numerous space medical findings, critically identifies challenges and gaps, and puts the achievements into perspective toward long-term space traveling and also adding benefits to our home planet. The medical contents are trifold structured, starting with the well-being of space travelers (astronaut health studies), followed by medical formulation research under space conditions, and then concluding with a blueprint for space pharmaceutical manufacturing. The review covers essential elements of our Earth-based pharmaceutical research such as drug discovery, drug and formulation stability, drug-organ interaction, drug disintegration/bioavailability/pharmacokinetics, pathogen virulence, genome mutation, and body's resistance. The information compiles clinical, medicinal, biological, and chemical research as well as fundamentals and practical applications.
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Affiliation(s)
- Quy Don Tran
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
| | - Vienna Tran
- Adelaide
Medical School, University of Adelaide, Adelaide 5005, Australia
| | - Li Shean Toh
- Faculty
of Science, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Philip M. Williams
- Faculty
of Science, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - Nam Nghiep Tran
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
- Department
of Chemical Engineering, Can Tho University, Can Tho 900000, Vietnam
| | - Volker Hessel
- School
of Chemical Engineering and Advanced Materials, University of Adelaide, Adelaide 5005, Australia
- Andy
Thomas Centre for Space Resources, University
of Adelaide, Adelaide 5005, Australia
- School of
Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
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Timofeev VI, Abramchik YA, Muravyova TI, Zhukhlistova NE, Esipov RS, Kuranova IP. Three-Dimensional Structure of Recombinant Thermophilic Ribokinase from Thermus speсies 2.9 in Complex with Adenosine Diphosphate. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Comparison of Spatial Structures and Packaging of Phosphorybosil Pyrophosphate Synthetase 2 from Thermus thermophilus HB27 in Rhombohedral and Tetragonal Crystals. CRYSTALS 2021. [DOI: 10.3390/cryst11091128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report the spatial structure of phosphoribosyl pyrophosphate synthetase 2 from the thermophilic bacterium Thermus thermophilus HB27 (TthPRPPS2) obtained at a 1.85 Å resolution using a diffraction set collected from rhombohedral crystals (space group R32-h), grown with lithium sulfate as a precipitant. This crystal structure was compared with the structure of TthPRPPS2, previously obtained at a 2.2 Å resolution using diffraction sets from the tetragonal crystals (space group P41212), grown with ammonium sulfate as a precipitant. The comparison of these structures allows the study of the differences between protein molecules in both crystalline structures, as well as the packaging of enzyme molecules in crystals of both spatial groups. Our results may contribute to the research of the structural basis of catalytic activity and substrate specificity of this enzyme.
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Akparov VK, Konstantinova GE, Timofeev VI, Kuranova IP, Khaliullin IG. Preparation, Crystallization, and Preliminary X-Ray Diffraction Study of Mutant Carboxypeptidase T Bearing the Primary Specificity Pocket and the Active-Site Loop of Carboxypeptidase B. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s106377452006005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Timofeev VI, Zhukhlistova NE, Kuranova IP. Crystal Packing of Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis in Two Crystal Modifications. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520010265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Akparov VK, Timofeev VI, Konstantinova GE, Khaliullin IG, Kuranova IP, Rakitina TV, Švedas V. The nature of the ligand's side chain interacting with the S1'-subsite of metallocarboxypeptidase T (from Thermoactinomyces vulgaris) determines the geometry of the tetrahedral transition complex. PLoS One 2019; 14:e0226636. [PMID: 31887148 PMCID: PMC6937156 DOI: 10.1371/journal.pone.0226636] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/27/2019] [Indexed: 01/03/2023] Open
Abstract
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.
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Affiliation(s)
- Valery Kh. Akparov
- Protein Chemistry Department, Federal Institution "State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia
- Protein Factory, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Vladimir I. Timofeev
- Laboratory of X-ray analysis methods and synchrotron radiation, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- Kurchatov center of synchrotron-neutron research, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Galina E. Konstantinova
- Protein Chemistry Department, Federal Institution "State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", Moscow, Russia
| | - Ilyas G. Khaliullin
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | - Inna P. Kuranova
- Laboratory of X-ray analysis methods and synchrotron radiation, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Moscow, Russia
- Kurchatov center of synchrotron-neutron research, National Research Centre “Kurchatov Institute”, Moscow, Russia
| | - Tatiana V. Rakitina
- Protein Factory, National Research Centre “Kurchatov Institute”, Moscow, Russia
- Laboratory of Hormonal Regulation Proteins, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vytas Švedas
- Faculty of Bioengineering and Bioinformatics, Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Akparov VK, Timofeev VI, Korzhenevskiy DA, Kuranova IP, Rakitina TV. Three-Dimensional Structure of a Mutant of Carboxypeptidase T from Thermoactinomyces vulgaris Bearing an Implanted S1' Subsite of Pancreatic Carboxypeptidase B Complexed with a Product Analog. CRYSTALLOGR REP+ 2019. [DOI: 10.1134/s1063774519040035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Akparov VK, Timofeev VI, Khaliullin IG, Konstantinova GE, Kuranova IP, Rakitina TV, Švedas VK. Mobile Loop in the Active Site of Metallocarboxypeptidases as an Underestimated Determinant of Substrate Specificity. BIOCHEMISTRY (MOSCOW) 2019; 83:1594-1602. [PMID: 30878033 DOI: 10.1134/s0006297918120167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
- V Kh Akparov
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia.
| | - V I Timofeev
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Center, Russian Academy of Sciences, Moscow, 119333, Russia. .,Kurchatov Institute National Research Center, Moscow, 123098, Russia
| | - I G Khaliullin
- Laboratory of Ion and Molecular Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700, Russia.
| | - G E Konstantinova
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia
| | - I P Kuranova
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Center, Russian Academy of Sciences, Moscow, 119333, Russia. .,Kurchatov Institute National Research Center, Moscow, 123098, Russia
| | - T V Rakitina
- Kurchatov Institute National Research Center, Moscow, 123098, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Hormonal Regulation Proteins, Russian Academy of Sciences, Moscow, 117997, Russia
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Akparov VK, Timofeev VI, Kuranova IP, Rakitina TV. Crystal structure of mutant carboxypeptidase T from Thermoactinomyces vulgaris with an implanted S1' subsite from pancreatic carboxypeptidase B. Acta Crystallogr F Struct Biol Commun 2018; 74:638-643. [PMID: 30279315 PMCID: PMC6168770 DOI: 10.1107/s2053230x18011962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/23/2018] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Valery Kh. Akparov
- Protein Chemistry Department, State Research Institute for Genetics and Selection of Industrial Microorganisms, 1yi Dorozhnyi Proezd 1, Moscow 117545, Russian Federation
| | - Vladimir I. Timofeev
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatova Sq. 1, Moscow 123182, Russian Federation
| | - Inna P. Kuranova
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospect 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatova Sq. 1, Moscow 123182, Russian Federation
| | - Tatiana V. Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatova Sq. 1, Moscow 123182, Russian Federation
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Sinitsyna EV, Timofeev VI, Zhukhlistova NE, Muravieva TI, Kostromina MA, Esipov RS, Kuranova IP. Crystallization and Preliminary X-ray Diffraction Study of Purine Nucleoside Phosphorylase from the Thermophilic Bacterium Thermus thermophilus Strain HB27. CRYSTALLOGR REP+ 2018. [DOI: 10.1134/s1063774518050279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Timofeev VI, Zhukhlistova NE, Abramchik YA, Muravieva TI, Esipov RS, Kuranova IP. Crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with acyclovir. Acta Crystallogr F Struct Biol Commun 2018; 74:402-409. [PMID: 29969103 PMCID: PMC6038453 DOI: 10.1107/s2053230x18008087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/31/2018] [Indexed: 11/10/2022] Open
Abstract
Escherichia coli purine nucleoside phosphorylase (PNP), which catalyzes the reversible phosphorolysis of purine ribonucleosides, belongs to the family I hexameric PNPs. Owing to their key role in the purine salvage pathway, PNPs are attractive targets for drug design against some pathogens. Acyclovir (ACV) is an acyclic derivative of the PNP substrate guanosine and is used as an antiviral drug for the treatment of some human viral infections. The crystalline complex of E. coli PNP with acyclovir was prepared by co-crystallization in microgravity using counter-diffusion through a gel layer in a capillary. The structure of the E. coli PNP-ACV complex was solved at 2.32 Å resolution using the molecular-replacement method. The ACV molecule is observed in two conformations and sulfate ions were located in both the nucleoside-binding and phosphate-binding pockets of the enzyme. A comparison with the complexes of other hexameric and trimeric PNPs with ACV shows the similarity in acyclovir binding by these enzymes.
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Affiliation(s)
- Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Nadezhda E. Zhukhlistova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
| | - Yuliya A. Abramchik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Tatiana I. Muravieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Roman S. Esipov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
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Timofeev VI, Zhukhlistova NE, Abramchik YA, Fateev II, Kostromina MA, Muravieva TI, Esipov RS, Kuranova IP. Crystal structure of Escherichia coli purine nucleoside phosphorylase in complex with 7-deazahypoxanthine. Acta Crystallogr F Struct Biol Commun 2018; 74:355-362. [PMID: 29870020 PMCID: PMC5987744 DOI: 10.1107/s2053230x18006337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/25/2018] [Indexed: 11/10/2022] Open
Abstract
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 recombinant Escherichia coli PNP (EcPNP) with an inhibition constant Ki of 0.13 mM. A crystal of EcPNP in complex with 7DHX was obtained in microgravity by the counter-diffusion technique and the three-dimensional structure of the EcPNP-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 group P6122, with unit-cell parameters a = 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 the EcPNP active site are discussed.
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Affiliation(s)
- Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Nadezhda E. Zhukhlistova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
| | - Yuliya A. Abramchik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Ilya I. Fateev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Maria A. Kostromina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Tatiana I. Muravieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Roman S. Esipov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- Kurchatov Complex of NBICS-Technologies, National Research Center ‘Kurchatov Institute’, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
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Sinitsyna EV, Timofeev VI, Tuzova ES, Kostromina MA, Murav’eva TI, Esipov RS, Kuranova IP. Crystallization and preliminary X-ray diffraction study of recombinant adenine phosphoribosyltransferase from the thermophilic bacterium Thermus thermophilus strain HB27. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s106377451704023x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Timofeev VI, Sinitsyna EV, Kostromina MA, Muravieva TI, Makarov DA, Mikheeva OO, Kuranova IP, Esipov RS. Crystal structure of recombinant phosphoribosylpyrophosphate synthetase 2 from Thermus thermophilus HB27 complexed with ADP and sulfate ions. Acta Crystallogr F Struct Biol Commun 2017; 73:369-375. [PMID: 28580926 PMCID: PMC5458395 DOI: 10.1107/s2053230x17007488] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/20/2017] [Indexed: 11/10/2022] Open
Abstract
Phosphoribosylpyrophosphate synthetase (PRPPS) from the thermophilic bacterial strain Thermus thermophilus HB27 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 in T. thermophilus PRPPS. 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.
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Affiliation(s)
- Vladimir I. Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- National Research Center ‘Kurchatov Institute’, Kurchatov Complex of NBICS-Technologies, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Ekaterina V. Sinitsyna
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Maria A. Kostromina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Tatiana I. Muravieva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Dmitry A. Makarov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Olga O. Mikheeva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre ‘Crystallography and Photonics’ of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation
- National Research Center ‘Kurchatov Institute’, Kurchatov Complex of NBICS-Technologies, Akad. Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Roman S. Esipov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation
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Akparov V, Timofeev V, Khaliullin I, Švedas V, Kuranova I. Structure of the carboxypeptidase B complex with N-sulfamoyl-L-phenylalanine – a transition state analog of non-specific substrate. J Biomol Struct Dyn 2017; 36:956-965. [DOI: 10.1080/07391102.2017.1304242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Valery Akparov
- Protein Chemistry Department, State Research Institute for Genetics and Selection of Industrial Microorganisms, 1-yi DorozhnyiProezd 1, Moscow, 117545, Russia
| | - Vladimir Timofeev
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskii Prospect 59, Moscow, 119333, Russia
- NBICS Center, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatov Sq. 1, Moscow, 123182, Russia
| | - Ilyas Khaliullin
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology (State University), 9 Institutsky per. Dolgoprudny, Moscow, 141700, Russia
| | - Vytas Švedas
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 1/40Leninskie Gory, Moscow, 119991, Russia
| | - Inna Kuranova
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” of Russian Academy of Sciences, Leninskii Prospect 59, Moscow, 119333, Russia
- NBICS Center, National Research Centre ‘Kurchatov Institute’, Akad. Kurchatov Sq. 1, Moscow, 123182, Russia
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Akparov VK, Timofeev VI, Maghsoudi NN, Kuranova IP. Three-dimensional structure of porcine pancreatic carboxypeptidase B with an acetate ion and two zinc atoms in the active site. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s106377451702002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abramchik YA, Timofeev VI, Muravieva TI, Sinitsyna EV, Esipov RS, Kuranova IP. Crystallization and preliminary X-ray diffraction analysis of recombinant phosphoribosylpyrophosphate synthetase from the Thermophilic thermus thermophilus strain HB27. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517010035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abramchik YA, Timofeev VI, Muravieva TI, Esipov RS, Kuranova IP. Crystallization and preliminary X-ray diffraction study of recombinant ribokinase from Thermus Species 2.9. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s106377451606002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Boyko KM, Timofeev VI, Samygina VR, Kuranova IP, Popov VO, Koval’chuk MV. Protein crystallization under microgravity conditions. Analysis of the results of Russian experiments performed on the International Space Station in 2005−2015. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516050059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Timofeev VI, Abramchik YA, Zhukhlistova NE, Muravieva TI, Esipov RS, Kuranova IP. Three-dimensional structure of E. Coli purine nucleoside phosphorylase at 0.99 Å resolution. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516020292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Timofeev VI, Abramchik YA, Zhukhlistova NE, Muravieva TI, Esipov RS, Kuranova IP. Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 Å resolution. CRYSTALLOGR REP+ 2016. [DOI: 10.1134/s1063774516010247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Akparov V, Sokolenko N, Timofeev V, Kuranova I. Structure of the complex of carboxypeptidase B and N-sulfamoyl-L-arginine. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1335-40. [PMID: 26457527 DOI: 10.1107/s2053230x15016799] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/08/2015] [Indexed: 11/11/2022]
Abstract
Porcine pancreatic carboxypeptidase B (EC 3.4.23.6) was complexed with a stable transition-state analogue, N-sulfamoyl-L-arginine, in which an S atom imitates the sp(3)-hybridized carbon in the scissile-bond surrogate. Crystals were grown in a form belonging to the same space group, P41212, as the uncomplexed enzyme. X-ray data were collected to a resolution of 1.25 Å. The molecule was refined and the positions of non-H atoms of the inhibitor and water molecules were defined using difference Fourier maps. The enzyme-inhibitor complex and 329 water molecules were further refined to a crystallographic R factor of 0.159. The differences in conformation between the complexed and uncomplexed forms of carboxypeptidase B are shown. The inhibitor is bound in a curved conformation in the active-site cleft, and the sulfamide group is bound to the Zn ion in an asymmetric bidentate fashion. The complex is stabilized by hydrogen bonds between the N1/N2 guanidine group of the inhibitor and the Asp255 carboxyl of the enzyme. The side-chain CH2 groups of the inhibitor are in van der Waals contact with Leu203 and Ile247 in the enzyme. This study provides useful clues concerning how the transition state of arginine may bind to carboxypeptidase B and therefore provides an insight into the structural basis of carboxypeptidase B selectivity, which is useful for the rational design of a carboxypeptidase with improved selectivity for industrial recombinant pro-insulin processing.
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Affiliation(s)
- Valery Akparov
- Protein Chemistry Department, State Research Institute for Genetics and Selection of Industrial Microorganisms, 1yi Dorozhnyi Proezd 1, 117545 Moscow, Russian Federation
| | - Nikolay Sokolenko
- Chemical Synthesis Department, Innovation Research Centre `Solaris', Tallinskaya str. 32-2-44, 123458 Moscow, Russian Federation
| | - Vladimir Timofeev
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, 119333 Moscow, Russian Federation
| | - Inna Kuranova
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, 119333 Moscow, Russian Federation
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Timofeev VI, Abramchik YA, Zhukhlistova NE, Kuranova IP. Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. Coli. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515050181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Boyko KM, Popov VO, Kovalchuk MV. Promising approaches to crystallization of macromolecules suppressing the convective mass transport to the growing crystal. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4557] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Timofeev VI, Chupova LA, Esipov RS, Kuranova IP. Crystallization and preliminary X-ray diffraction study of phosphopantetheine adenylyltransferase from M. tuberculosis crystallizing in space group P32. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s106377451505017x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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27
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Timofeev V, Slutskaya E, Gorbacheva M, Boyko K, Rakitina T, Korzhenevskiy D, Lipkin A, Popov V. Structure of recombinant prolidase from Thermococcus sibiricus in space group P21221. Acta Crystallogr F Struct Biol Commun 2015; 71:951-7. [PMID: 26249680 PMCID: PMC4528922 DOI: 10.1107/s2053230x15009498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/18/2015] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of recombinant prolidase from Thermococcus sibiricus was determined by X-ray diffraction at a resolution of 2.6 Å and was found to contain a tetramer in the asymmetric unit. A protein crystal grown in microgravity using the counter-diffusion method was used for X-ray studies. The crystal belonged to space group P21221, with unit-cell parameters a = 97.60, b = 123.72, c = 136.52 Å, α = β = γ = 90°. The structure was refined to an Rcryst of 22.1% and an Rfree of 29.6%. The structure revealed flexible folding of the N-terminal domain of the protein as well as high variability in the positions of the bound metal ions. The coordinates of the resulting model were deposited in the Protein Data Bank as entry 4rgz.
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Affiliation(s)
- Vladimir Timofeev
- Protein Factory, National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova Square 1, Moscow 123182, Russian Federation
- X-ray Analysis Methods and Synchrotron Radiation Laboratory, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninskii Prospekt 59, Moscow 119333, Russian Federation
| | - Elvira Slutskaya
- Laboratory of Enzyme Engineering, Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii Prospekt 33, Moscow 119071, Russian Federation
| | - Marina Gorbacheva
- Protein Factory, National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova Square 1, Moscow 123182, Russian Federation
- Laboratory of Enzyme Engineering, Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii Prospekt 33, Moscow 119071, Russian Federation
| | - Konstantin Boyko
- Protein Factory, National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova Square 1, Moscow 123182, Russian Federation
- Laboratory of Enzyme Engineering, Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii Prospekt 33, Moscow 119071, Russian Federation
| | - Tatiana Rakitina
- Protein Factory, National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova Square 1, Moscow 123182, Russian Federation
- Laboratory of Hormonal Regulation Proteins, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Dmitry Korzhenevskiy
- Protein Factory, National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Alexey Lipkin
- Protein Factory, National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova Square 1, Moscow 123182, Russian Federation
| | - Vladimir Popov
- Protein Factory, National Research Centre ‘Kurchatov Institute’, Akademika Kurchatova Square 1, Moscow 123182, Russian Federation
- Laboratory of Enzyme Engineering, Bach Institute of Biochemistry, Russian Academy of Sciences, Leninskii Prospekt 33, Moscow 119071, Russian Federation
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Abramchik YA, Timofeev VI, Zhukhlistova NE, Muravieva TI, Esipov RS, Kuranova IP. Purification, crystallization, and preliminary X-ray diffraction study of purine nucleoside phosphorylase from E. coli. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515040021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Akparov VK, Timofeev VI, Kuranova IP. Crystallization and preliminary X-ray diffraction study of porcine carboxypeptidase B. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515030025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Akparov VK, Timofeev VI, Khaliullin IG, Švedas V, Chestukhina GG, Kuranova IP. Structural insights into the broad substrate specificity of carboxypeptidase T fromThermoactinomyces vulgaris. FEBS J 2015; 282:1214-24. [DOI: 10.1111/febs.13210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/19/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Valery Kh. Akparov
- State Research Institute for Genetics and Selection of Industrial Microorganisms; Moscow Russia
| | - Vladimir I. Timofeev
- Shubnikov Institute of Crystallography; Russian Academy of Sciences; Moscow Russia
| | - Ilyas G. Khaliullin
- Belozersky Institute of Physicochemical Biology; Lomonosov Moscow State University; Russia
- Moscow Institute of Physics and Technology (State University); Russia
| | - Vytas Švedas
- Belozersky Institute of Physicochemical Biology; Lomonosov Moscow State University; Russia
| | - Galina G. Chestukhina
- State Research Institute for Genetics and Selection of Industrial Microorganisms; Moscow Russia
| | - Inna P. Kuranova
- Shubnikov Institute of Crystallography; Russian Academy of Sciences; Moscow Russia
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Baskakova SS, Kovalyov SI, Kramarenko VA, Zadorozhnaya LA, Lyasnikova MS, Dymshits YM, Shishkov VA, Egorov AV, Dolgin AM, Voloshin AE, Kovalchuk MV. New scientific equipment for protein crystallization in microgravity, BELKA, and its approbation on the Bion-M No. 1 spacecraft. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Strelov VI, Kuranova IP, Zakharov BG, Voloshin AE. Crystallization in space: Results and prospects. CRYSTALLOGR REP+ 2014. [DOI: 10.1134/s1063774514060285] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Timofeev V, Abramchik Y, Zhukhlistova N, Muravieva T, Fateev I, Esipov R, Kuranova I. 3'-Azidothymidine in the active site of Escherichia coli thymidine phosphorylase: the peculiarity of the binding on the basis of X-ray study. ACTA ACUST UNITED AC 2014; 70:1155-65. [PMID: 24699659 DOI: 10.1107/s1399004714001904] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 01/27/2014] [Indexed: 11/10/2022]
Abstract
The structural study of complexes of thymidine phosphorylase (TP) with nucleoside analogues which inhibit its activity is of special interest because many of these compounds are used as chemotherapeutic agents. Determination of kinetic parameters showed that 3'-azido-3'-deoxythymidine (3'-azidothymidine; AZT), which is widely used for the treatment of human immunodeficiency virus, is a reversible noncompetitive inhibitor of Escherichia coli thymidine phosphorylase (TP). The three-dimensional structure of E. coli TP complexed with AZT was solved by the molecular-replacement method and was refined at 1.52 Å resolution. Crystals for X-ray study were grown in microgravity by the counter-diffusion technique from a solution of the protein in phosphate buffer with ammonium sulfate as a precipitant. The AZT molecule was located with full occupancy in the electron-density maps in the nucleoside-binding pocket of TP, whereas the phosphate-binding pocket of the enzyme was occupied by phosphate (or sulfate) ion. The structure of the active-site cavity and conformational changes of the enzyme upon AZT binding are described in detail. It is found that the position of AZT differs remarkably from the positions of the pyrimidine bases and nucleoside analogues in other known complexes of pyrimidine phosphorylases, but coincides well with the position of 2'-fluoro-3'-azido-2',3'-dideoxyuridine (N3FddU) in the recently investigated complex of E. coli TP with this ligand (Timofeev et al., 2013). The peculiarities of the arrangement of N3FddU and 3'-azidothymidine in the nucleoside binding pocket of TP and correlations between the arrangement and inhibitory properties of these compounds are discussed.
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Affiliation(s)
- Vladimir Timofeev
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
| | - Yulia Abramchik
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
| | - Nadezda Zhukhlistova
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
| | - Tatiana Muravieva
- Laboratory of Biotechnology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Ilya Fateev
- Laboratory of Biotechnology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Roman Esipov
- Laboratory of Biotechnology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Inna Kuranova
- X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, 119333, Russian Federation
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Timofeev VI, Abramchik YA, Fateev IV, Zhukhlistova NE, Murav’eva TI, Kuranova IP, Esipov RS. Three-dimensional structure of thymidine phosphorylase from E. coli in complex with 3′-azido-2′-fluoro-2′,3′-dideoxyuridine. CRYSTALLOGR REP+ 2013. [DOI: 10.1134/s1063774513060230] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Timofeev V, Smirnova E, Chupova L, Esipov R, Kuranova I. X-ray study of the conformational changes in the molecule of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis during the catalyzed reaction. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1660-70. [PMID: 23151631 DOI: 10.1107/s0907444912040206] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/22/2012] [Indexed: 11/11/2022]
Abstract
Structures of recombinant phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium 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 C(α) atoms. 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.
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Affiliation(s)
- Vladimir Timofeev
- Laboratory of X-ray Analysis Methods and Synchrotron Radiation, Shubnikov Institute of Crystallography, Russian Academy of Sciences, Leninsky Prospect 59, Moscow, Russian Federation.
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Timofeev VI, Smirnova EA, Chupova LA, Esipov RS, Kuranova IP. Three-dimensional structure of phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis in the apo form and in complexes with coenzyme A and dephosphocoenzyme A. CRYSTALLOGR REP+ 2012. [DOI: 10.1134/s1063774512010142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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