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Veiko VP, Antipov AN, Mordkovich NN, Okorokova NA, Safonova TN, Polyakov KM. The Thermostability of Nucleoside Phosphorylases from Prokaryotes. I. The Role of the Primary Structure of the N-terminal fragment of the Protein in the Thermostability of Uridine Phosphorylases. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822060151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
AbstractMutant uridine phosphorylase genes from Shewanella oneidensis MR-1 (S. oneidensis) were constructed by site-directed mutagenesis and strains-producers of the corresponding recombinant (F5I and F5G) proteins were obtained on the basis of Escherichia coli cells. The mutant proteins were purified and their physicochemical and enzymatic properties were studied. It was shown that the N-terminal fragment of uridine phosphorylase plays an important role in the thermal stabilization of the enzyme as a whole. The role of the aminoacid (a.a.) residue phenylalanine (F5) in the formation of thermotolerance of uridine phosphorylases from gamma-proteobacteria was revealed.
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2
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Polyakov KM, Mordkovich NN, Safonova TN, Antipov AN, Okorokova NA, Dorovatovskii PV, Veiko VP. Role of Conformational Changes of Hexameric Bacterial Uridine Phosphorylases in Substrate Binding. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050199] [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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3
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Snell EH, Helliwell JR. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight. CRYSTALLOGR REV 2021. [DOI: 10.1080/0889311x.2021.1900833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- E. H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
- Materials Design and Innovation Department, SUNY Buffalo, Buffalo, NY, USA
| | - J. R. Helliwell
- Chemistry Department, University of Manchester, Manchester, UK
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Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases. Biomolecules 2020; 10:biom10040552. [PMID: 32260512 PMCID: PMC7226091 DOI: 10.3390/biom10040552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 11/28/2022] Open
Abstract
Nucleoside phosphorylases catalyze the reversible phosphorolysis of nucleosides to heterocyclic bases, giving α-d-ribose-1-phosphate or α-d-2-deoxyribose-1-phosphate. These enzymes are involved in salvage pathways of nucleoside biosynthesis. The level of these enzymes is often elevated in tumors, which can be used as a marker for cancer diagnosis. This review presents the analysis of conformations of nucleosides and their analogues in complexes with nucleoside phosphorylases of the first (NP-1) family, which includes hexameric and trimeric purine nucleoside phosphorylases (EC 2.4.2.1), hexameric and trimeric 5′-deoxy-5′-methylthioadenosine phosphorylases (EC 2.4.2.28), and uridine phosphorylases (EC 2.4.2.3). Nucleosides adopt similar conformations in complexes, with these conformations being significantly different from those of free nucleosides. In complexes, pentofuranose rings of all nucleosides are at the W region of the pseudorotation cycle that corresponds to the energy barrier to the N↔S interconversion. In most of the complexes, the orientation of the bases with respect to the ribose is in the high-syn region in the immediate vicinity of the barrier to syn ↔ anti transitions. Such conformations of nucleosides in complexes are unfavorable when compared to free nucleosides and they are stabilized by interactions with the enzyme. The sulfate (or phosphate) ion in the active site of the complexes influences the conformation of the furanose ring. The binding of nucleosides in strained conformations is a characteristic feature of the enzyme–substrate complex formation for this enzyme group.
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Wako H, Endo S. Dynamic properties of oligomers that characterize low-frequency normal modes. Biophys Physicobiol 2019; 16:220-231. [PMID: 31984175 PMCID: PMC6976002 DOI: 10.2142/biophysico.16.0_220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/09/2019] [Indexed: 01/09/2023] Open
Abstract
Dynamics of oligomeric proteins (one trimer, two tetramers, and one hexamer) were studied by elastic network model-based normal mode analysis to characterize their large-scale concerted motions. First, the oligomer motions were simplified by considering rigid-body motions of individual subunits. The subunit motions were resolved into three components in a cylindrical coordinate system: radial, tangential, and axial ones. Single component is dominant in certain normal modes. However, more than one component is mixed in others. The subunits move symmetrically in certain normal modes and as a standing wave with several wave nodes in others. Secondly, special attention was paid to atoms on inter-subunit interfaces. Their displacement vectors were decomposed into intra-subunit deformative (internal) and rigid-body (external) motions in individual subunits. The fact that most of the cosines of the internal and external motion vectors were negative for the atoms on the inter-subunit interfaces, indicated their opposing movements. Finally, a structural network of residues defined for each normal mode was investigated; the network was constructed by connecting two residues in contact and moving coherently. The centrality measure “betweenness” of each residue was calculated for the networks. Several residues with significantly high betweenness were observed on the inter-subunit interfaces. The results indicate that these residues are responsible for oligomer dynamics. It was also observed that amino acid residues with significantly high betweenness were more conservative. This supports that the betweenness is an effective characteristic for identifying an important residue in protein dynamics.
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Affiliation(s)
- Hiroshi Wako
- School of Social Sciences, Waseda University, Shinjuku-ku, Tokyo 169-8050, Japan
| | - Shigeru Endo
- Department of Physics, School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
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Talaat HM, Ibrahim IT, Bayomy NA, Farouk N. Synthesis of 99mTc-Radiolabeled Uridine as a Potential Tumor Imaging Agent. RADIOCHEMISTRY 2018. [DOI: 10.1134/s1066362218010095] [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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7
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Mordkovich NN, Safonova TN, Antipov AN, Manuvera VA, Polyakov KM, Okorokova NA, Veiko VP. Study of Structural-Functional Organization of Nucleoside Phosphorylases of Gammaproteobacteria. Special Aspects of Functioning of Uridine Phosphorylase Phosphate-Binding Site. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818010064] [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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8
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Alexeev CS, Sivets GG, Safonova TN, Mikhailov SN. Substrate specificity of E. coli uridine phosphorylase. Further evidences of high-syn conformation of the substrate in uridine phosphorolysis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 36:107-121. [PMID: 27846376 DOI: 10.1080/15257770.2016.1223306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Twenty five uridine analogues have been tested and compared with uridine with respect to their potency to bind to E. coli uridine phosphorylase. The kinetic constants of the phosphorolysis reaction of uridine derivatives modified at 2'-, 3'- and 5'-positions of the sugar moiety and 2-, 4-, 5- and 6-positions of the heterocyclic base were determined. The absence of the 2'- or 5'-hydroxyl group is not crucial for the successful binding and phosphorolysis. On the other hand, the absence of both the 2'- and 5'-hydroxyl groups leads to the loss of substrate binding to the enzyme. The same effect was observed when the 3'-hydroxyl group is absent, thus underlining the key role of this group. Our data shed some light on the mechanism of ribo- and 2'-deoxyribonucleoside discrimination by E. coli uridine phosphorylase and E. coli thymidine phosphorylase. A comparison of the kinetic results obtained in the present study with the available X-ray structures and analysis of hydrogen bonding in the enzyme-substrate complex demonstrates that uridine adopts an unusual high-syn conformation in the active site of uridine phosphorylase.
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Affiliation(s)
- C S Alexeev
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia
| | - G G Sivets
- b Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus , Minsk , Belarus
| | - T N Safonova
- c Bach Institute of Biochemistry, Russian Academy of Sciences , Moscow , Russia
| | - S N Mikhailov
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia
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9
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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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10
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Balaev VV, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine. Acta Crystallogr F Struct Biol Commun 2016; 72:224-33. [PMID: 26919527 PMCID: PMC4774882 DOI: 10.1107/s2053230x1600162x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/26/2016] [Indexed: 11/10/2022] Open
Abstract
Highly specific thymidine phosphorylases catalyze the phosphorolytic cleavage of thymidine, with the help of a phosphate ion, resulting in thymine and 2-deoxy-α-D-ribose 1-phosphate. Thymidine phosphorylases do not catalyze the phosphorolysis of uridine, in contrast to nonspecific pyrimidine nucleoside phosphorylases and uridine phosphorylases. Understanding the mechanism of substrate specificity on the basis of the nucleoside is essential to support rational drug-discovery investigations of new antitumour and anti-infective drugs which are metabolized by thymidine phosphorylases. For this reason, X-ray structures of the thymidine phosphorylase from Salmonella typhimurium were solved and refined: the unliganded structure at 2.05 Å resolution (PDB entry 4xr5), the structure of the complex with thymidine at 2.55 Å resolution (PDB entry 4yek) and that of the complex with uridine at 2.43 Å resolution (PDB entry 4yyy). The various structural features of the enzyme which might be responsible for the specificity for thymidine and not for uridine were identified. The presence of the 2'-hydroxyl group in uridine results in a different position of the uridine furanose moiety compared with that of thymidine. This feature may be the key element of the substrate specificity. The specificity might also be associated with the opening/closure mechanism of the two-domain subunit structure of the enzyme.
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Affiliation(s)
- Vladislav V. Balaev
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Alexander A. Lashkov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Azat G. Gabdulkhakov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Maria V. Dontsova
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
| | - Tatiana A. Seregina
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | - Alexander S. Mironov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1-st Dorozhny Proezd 1, Moscow 117545, Russian Federation
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, Institute of Biochemistry and Molecular Biology, c/o DESY, Building 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Al’bert M. Mikhailov
- A. V. Shubnikov Institute of Crystallography, Leninsky Prospect 59, Moscow 119333, Russian Federation
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11
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Safonova TN, Mordkovich NN, Veiko VP, Okorokova NA, Manuvera VA, Dorovatovskii PV, Popov VO, Polyakov KM. Concerted action of two subunits of the functional dimer of Shewanella oneidensis MR-1 uridine phosphorylase derived from a comparison of the C212S mutant and the wild-type enzyme. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:203-10. [PMID: 26894668 DOI: 10.1107/s2059798315024353] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022]
Abstract
Uridine phosphorylase (UP; EC 2.4.2.3), a key enzyme in the pyrimidine-salvage pathway, catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The structure of the C212S mutant of uridine phosphorylase from the facultatively aerobic Gram-negative γ-proteobacterium Shewanella oneidensis MR-1 (SoUP) was determined at 1.68 Å resolution. A comparison of the structures of the mutant and the wild-type enzyme showed that one dimer in the mutant hexamer differs from all other dimers in the mutant and wild-type SoUP (both in the free form and in complex with uridine). The key difference is the `maximum open' state of one of the subunits comprising this dimer, which has not been observed previously for uridine phosphorylases. Some conformational features of the SoUP dimer that provide access of the substrate into the active site are revealed. The binding of the substrate was shown to require the concerted action of two subunits of the dimer. The changes in the three-dimensional structure induced by the C212S mutation account for the lower affinity of the mutant for inorganic phosphate, while the affinity for uridine remains unchanged.
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Affiliation(s)
- T N Safonova
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - N N Mordkovich
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - V P Veiko
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - N A Okorokova
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - V A Manuvera
- Scientific Research Institute of Physical-Chemical Medicine, Federal Medical-Biological Agency, 1a Malaya Pirogovskaya St., Moscow 119435, Russian Federation
| | - P V Dorovatovskii
- National Research Centre `Kurchatov Institute', 1 Pl. Akademika Kurchatova, Moscow 123182, Russian Federation
| | - V O Popov
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
| | - K M Polyakov
- Bach Institute of Biochemistry, Russian Academy of Sciences, 33 Leninskii Ave., Moscow 119071, Russian Federation
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12
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Youn HS, Kim TG, Kim MK, Kang GB, Kang JY, Lee JG, An JY, Park KR, Lee Y, Im YJ, Lee JH, Eom SH. Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis. Sci Rep 2016; 6:19681. [PMID: 26805589 PMCID: PMC4726147 DOI: 10.1038/srep19681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/14/2015] [Indexed: 11/09/2022] Open
Abstract
Quinolinate phosphoribosyltransferase (QPRT) catalyses the production of nicotinic
acid mononucleotide, a precursor of de novo biosynthesis of the ubiquitous
coenzyme nicotinamide adenine dinucleotide. QPRT is also essential for maintaining
the homeostasis of quinolinic acid in the brain, a possible neurotoxin causing
various neurodegenerative diseases. Although QPRT has been extensively analysed, the
molecular basis of the reaction catalysed by human QPRT remains unclear. Here, we
present the crystal structures of hexameric human QPRT in the apo form and its
complexes with reactant or product. We found that the interaction between dimeric
subunits was dramatically altered during the reaction process by conformational
changes of two flexible loops in the active site at the dimer-dimer interface. In
addition, the N-terminal short helix α1 was identified as a critical
hexamer stabilizer. The structural features, size distribution, heat aggregation and
ITC studies of the full-length enzyme and the enzyme lacking helix α1
strongly suggest that human QPRT acts as a hexamer for cooperative reactant binding
via three dimeric subunits and maintaining stability. Based on our comparison of
human QPRT structures in the apo and complex forms, we propose a drug design
strategy targeting malignant glioma.
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Affiliation(s)
- Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Tae Gyun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Mun-Kyoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
| | - Young Jun Im
- College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, South Korea.,Department of Polar Sciences, Korea University of Science and Technology, Incheon 406-840, South Korea
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea.,Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 500-712, South Korea
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