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Akparov VK, Konstantinova GE, Timofeev VI, Kuranova IP. Preparation, Crystallization, and Preliminary X-Ray Diffraction Study of Mutant Carboxypeptidase T Bearing the Hydrophilized Primary Specificity Pocket. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521030020] [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, Konstantinova GE, Timofeev VI, Khaliullin IG, Kuranova IP. Structure of the microbial carboxypeptidase T complexed with the transition state analog N-sulfamoyl-l-lysine. Biophys Chem 2020; 270:106535. [PMID: 33412495 DOI: 10.1016/j.bpc.2020.106535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/19/2020] [Accepted: 12/19/2020] [Indexed: 11/18/2022]
Abstract
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.
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Affiliation(s)
- Valery Kh Akparov
- National Research Center "Kurchatov institute", Ak. Kurchatova square 1, Moscow 123182, Russian Federation.
| | - Galina E Konstantinova
- National Research Center "Kurchatov institute", Ak. Kurchatova square 1, Moscow 123182, Russian Federation
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" Russian Academy of Sciences, Leninskii Prospect 59, Moscow 119333, Russian Federation
| | - Ilyas G Khaliullin
- Moscow Institute of Physics and Technology (State University), 9 Institutsky per. Dolgoprudny, Moscow Region 141700, Russian Federation
| | - Inna P Kuranova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" Russian Academy of Sciences, Leninskii Prospect 59, Moscow 119333, Russian Federation
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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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Akparov VK, Timofeev VI, Khaliullin IG, Švedas V, Kuranova IP, Rakitina TV. Crystal structures of carboxypeptidase T complexes with transition-state analogs. J Biomol Struct Dyn 2017; 36:3958-3966. [DOI: 10.1080/07391102.2017.1404932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Valery Kh. Akparov
- Protein Chemistry Department, State Research Institute for Genetics and Selection of Industrial Microorganisms, 1yi Dorozhnyi Proezd, 1, Moscow 117545, Russia
| | - 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, Leninskii Prospect 59, Moscow 119333, Russia
- Kurchatov Complex of NBICS-Technologies, National Research Center “Kurchatov Institute”, Akad. Kurchatova pl.1, Moscow 123182, Russia
| | - Ilyas G. Khaliullin
- Laboratory of Ion and Molecular Physics, Moscow Institute of Physics and Technology, Institutskii per., 9, Dolgoprudnyi, Moscow Region 141700, Russia
| | - Vytas Švedas
- Biokinetics Department, Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie Gory 1, b.73, Moscow 119991, Russia
| | - 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, Leninskii Prospect 59, Moscow 119333, Russia
- Kurchatov Complex of NBICS-Technologies, National Research Center “Kurchatov Institute”, Akad. Kurchatova pl.1, Moscow 123182, Russia
| | - Tatiana V. Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Center “Kurchatov Institute”, Akad. Kurchatova pl.1, Moscow 123182, Russia
- Laboratory of Hormonal Regulation Proteins, M.M. Shemyakin and Yu.A, Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117997, Russia
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Timofeev VI, Kuznetsov SA, Akparov VK, Chestukhina GG, Kuranova IP. Three-dimensional structure of carboxypeptidase T from Thermoactinomyces vulgaris in complex with N-BOC-L-leucine. BIOCHEMISTRY (MOSCOW) 2013; 78:252-9. [PMID: 23586718 DOI: 10.1134/s0006297913030061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The 3D structure of recombinant bacterial carboxypeptidase T (CPT) in complex with N-BOC-L-leucine was determined at 1.38 Å resolution. Crystals for the X-ray study were grown in microgravity using the counter-diffusion technique. N-BOC-L-leucine and SO4(2-) ion bound in the enzyme active site were localized in the electron density map. Location of the leucine side chain in CPT-N-BOC-L-leucine complex allowed identification of the S1 subsite of the enzyme, and its structure was determined. Superposition of the structures of CPT-N-BOC-L-leucine complex and complexes of pancreatic carboxypeptidases A and B with substrate and inhibitors was carried out, and similarity of the S1 subsites in these three carboxypeptidases was revealed. It was found that SO4(2-) ion occupies the same position in the S1' subsite as the C-terminal carboxy group of the substrate.
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Affiliation(s)
- V I Timofeev
- Shubnikov Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia.
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Serkina AV, Zalunin IA, Levitin EI, Voejkova TA, Tyaglov BV, Novikova LM, Emeljanova LK, Konstantinova GE, Chestukhina GG. Carboxypeptidase from Streptomyces bikiniensis: primary structure, isolation, and properties. BIOCHEMISTRY. BIOKHIMIIA 2010; 75:1032-1038. [PMID: 21073425 DOI: 10.1134/s0006297910080122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A metallocarboxypeptidase produced by Streptomyces bikiniensis 27 strain (VKPM Ac-1783) (CPSb) was purified and characterized. The enzyme cleaves both basic and hydrophobic C-terminal amino acid residues from synthetic peptides, that is, it possesses specificity of mammalian carboxypeptidases A and B. The enzyme also hydrolyzes peptides bearing glutamic acid at the C-end. CPSb exhibits its maximal activity at pH 7.0-7.6 and 55°C. The nucleotide sequence encoding the mature CPSb in S. bikiniensis 27 (VKPM Ac-1783) genome (Accession No. GU362077) was determined. It is shown that the primary structure of the mature enzyme has a moderate degree of identity with orthologs from Streptomyces griseus (79% identity) and Streptomyces avermitilis (85% identity).
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Affiliation(s)
- A V Serkina
- Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia
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Grishin A, Akparov V, Chestukhina G. Structural principles of the broad substrate specificity of Thermoactinomyces vulgaris carboxypeptidase T--role of amino acid residues at positions 260 and 262. Protein Eng Des Sel 2008; 21:545-51. [DOI: 10.1093/protein/gzn031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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