Konstatin M Polyakov

Konstatin M Polyakov
Russian Academy of Sciences | RAS

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129
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1,395
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January 2009 - present
January 2002 - December 2012
Russian Academy of Sciences

Publications

Publications (129)
Article
Series of mutant genes of prokaryotic uridine phosphorylases (Shewanella oneidensis MR-1, Escherichia coli) were constructed, and the resulting strains-producers of the corresponding proteins were obtained. Proteins were purified, and their physicochemical and fermentative properties were studied. On the basis of the obtained data, the role of indi...
Article
Full-text available
The laccase from Steccherinum murashkinskyi is a member of the large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates, accompanied by the reduction of dioxygen to water. The reducing properties of X-ray radiation and the high quality of the laccase crystals allow the study of the catalyt...
Article
Full-text available
We present the functional and structural characterization of the first archaeal thermostable NADP-dependent aldehyde dehydrogenase AlDHPyr1147. In vitro , AlDHPyr1147 catalyzes the irreversible oxidation of short aliphatic aldehydes at 60–85°С, and the affinity of AlDHPyr1147 to the NADP+ at 60°С is comparable to that for mesophilic analogues at 25...
Data
Supplementary material contains (1) description of the determination of Kd values using Scatchard analysis; (2) Figures S1, S2 and S3(a,b) illustrating changes in the emission spectra of apo form of AlDHPyr1147 upon titration with coenzyme at 60°C; (3) Table S1 that lists conformations of the catalytic residues and the coenzyme in the models of AlD...
Article
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 1.6...
Article
Full-text available
Laccases belong to the class of multicopper oxidases catalyzing the oxidation of phenols accompanied by the reduction of molecular oxygen to water without the formation of hydrogen peroxide. The activity of laccases depends on the number of Cu atoms per enzyme molecule. The structure of type 2 copper-depleted laccase from Botrytis aclada has been s...
Article
Octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens catalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochrome c nitrite reductase directly in a crystal of...
Article
Full-text available
Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. A new laccase was isolated from the basidiomycete Coriolopsis caperata strain 0677 and its amino-acid sequence was determined. According to its physicochemi...
Article
Full-text available
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. Expression of UP from Shewanella oneidensis MR-1 (SoUP) was performed in Escherichia coli . The high-resolution X-ray structure of SoUP was solved in the free form and in comple...
Article
Full-text available
Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain four Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidi...
Conference Paper
Full-text available
Substrate specificity of E. coli uridine phosphorylase to pyrimidine nucleosides modified at 2’-, 3’- and 5’-positions of the sugar moiety and at 2-, 4-, 5- and 6-positions of the heterocyclic base was studied. The equilibrium (Keq) and kinetic constants for the phosphorolysis of nucleosides were measured. The most important hydrogen bonds in the e...
Article
Full-text available
Ribonuclease from Bacillus intermedius (binase) is a small basic protein with antitumour activity. The three-dimensional structure of the binase mutant form Glu43Ala/Phe81Ala was determined at 1.98 Å resolution and its functional properties, such as the kinetic parameters characterizing the hydrolysis of polyinosinic acid and cytotoxicity towards K...
Article
Full-text available
DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential for maintaining genome integrity in the replication, recombination and repair of DNA. High flexibility is important for the function of DNA ligase molecu...
Article
Prolidases are peptidases that are specific for dipeptides with proline as the second residue. The structure of recombinant prolidase from the hyperthermophilic archaeon Thermococcus sibiricus (Tsprol) was determined at 2.6 Å resolution. The homodimer of Tsprol is characterized by a complete lack of interactions between the N- and C-terminal domain...
Article
Uridine phosphorylase (UDP, EC 2.4.2.3), a key enzyme in the pyrimidine salvage pathway, catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. The gene expression of UDP from Shewanella oneidensis MR-1 was performed in the recipient strain Escherichia coli. The UDP protein was crystallized on earth (in the free form a...
Article
The gene xylE encoding endo-1,4-β-xylanase from the 10th family of glycosyl hydrolases produced by the mycelial fungus Penicillium canescens has been expressed under the control of the strong promoter of the bgaS gene encoding β-galactosidase from P. canescens. As a result, a strain-producer of endoxylanase XylE was developed. The recombinant enzym...
Article
Unlabelled: Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivibrio species was performed. It was shown that both enzymes have similar catalytic prope...
Article
Biochemical analysis of enantioselective short-chain alcohol dehydrogenase from the hyperthermophilic archaeon Thermococcus sibiricus (TsAdh319) revealed unique polyextremophilic properties of the enzyme - half-life of 1 h at 100 °C, tolerance to high salt (up to 4 M) and organic solvents (50% v/v) concentrations. To elucidate the molecular basis o...
Article
Octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR), like the previously characterized pentahaem nitrite reductases (NrfAs), catalyzes the six-electron reductions of nitrite to ammonia and of sulfite to sulfide. The active site of both TvNiR and NrfAs is formed by the lysine-coordinated haem and His, Tyr and Arg re...
Article
Full-text available
DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential to maintain the integrity of the genome in DNA replication, recombination and repair. A recombinant ATP-dependent DNA ligase from the hyperthermophilic a...
Article
Full-text available
Uridine phosphorylase (UDP, EC 2.4.2.3), a key enzyme in the pyrimidine salvage pathway, catalyses the reversible phosphorolysis of uridine to uracil and ribose 1‐phosphate. The gene expression of UDP from Shewanella oneidensis MR‐1 was performed in the recipient strain Escherichia coli. The UDP protein was crystallized on earth (in the free form a...
Article
This paper highlights a parallelization of the FMLSQ program, which allows full-matrix least-squares refinement of large macromolecular structures. The detailed elapsed time profiling of FMLSQ and analysis of its execution on two different Intel architectures has led to a dramatic speedup due to parallelization of all stages of the algorithm. Amdah...
Article
The structures of complexes of octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR) with the substrate sulfite (1.4 Å resolution; R(cryst) = 0.126) and the inhibitor cyanide (1.55 Å resolution; R(cryst) = 0.148) have been established. The complex with sulfite was prepared by the reduction of the protei...
Article
The structures of two crystal modifications of the W34F mutant ribonuclease from the bacterium Bacillus intermedius (binase) were solved and refined at 1.7 and 1.1 A resolution. The kinetic parameters of the hydrolysis of substrates of different lengths (GpU, GpUp, and poly(I)) by binase and its W34F mutant were investigated and compared. The catal...
Chapter
Octaheme cytochrome c nitrite reductase (TvNiR) from bacterium Thioalkalivibrio nitratireducens catalyzes the six-electron reduction of nitrite and two-electron reduction of hydroxylamine to ammonium without release of any intermediates. TvNiR also catalyzes the six-electron reduction of sulfite to sulfide. High-resolution structures of the TvNiR a...
Article
Full-text available
Alcohol dehydrogenases belong to the oxidoreductase family and play an important role in a broad range of physiological processes. They catalyze the cofactor-dependent reversible oxidation of alcohols to the corresponding aldehydes or ketones. The NADP-dependent short-chain alcohol dehydrogenase TsAdh319 from the thermophilic archaeon Thermococcus...
Article
Full-text available
Protealysin (PLN) belongs to the M4 family of peptidases that are commonly known as thermolysin-like proteases (TLPs). All TLPs are synthesized as precursors containing N-terminal propeptides. According to the primary structure of the N-terminal propeptides, the family is divided into two distinct groups. Representatives of the first group includin...
Article
Octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR) catalyzes the reduction of nitrite and hydroxylamine to ammonia. The structures of the free enzyme and of the enzyme in complexes with the substrate (nitrite ion) and the inhibitor (azide ion) have been solved previously. In this study we report the structures of...
Article
Full-text available
NAD(+)-dependent formate dehydrogenase (FDH) catalyzes the oxidation of formate ion to carbon dioxide coupled with the reduction of NAD(+) to NADH. The crystal structures of the apo and holo forms of FDH from the methylotrophic bacterium Moraxella sp. C-1 (MorFDH) are reported at 1.96 and 1.95 A resolution, respectively. MorFDH is similar to the pr...
Article
Full-text available
Protealysin (PLN) belongs to the M4 family of peptidases that are commonly known as thermolysin-like proteases (TLPs). All TLPs are synthesized as precursors containing N-terminal propeptides. According to the primary structure of the N-terminal propeptides, the family is divided into two distinct groups. Representatives of the first group includin...
Article
Full-text available
The crystal structure of the ternary complex of NAD+-dependent formate dehydrogenase from the methylotrophic bacterium Moraxella sp. C-1 with the cofactor (NAD+) and the inhibitor (azide ion) was established at 1.1 A resolution. The complex mimics the structure of the transition state of the enzymatic reaction. The structure was refined with anisot...
Article
Full-text available
It is supposed that α,γ-diketo acids (DKAs) inhibit the activity of hepatitis C virus RNA-dependent RNA poly-merase (RdRP HCV) via chelation of catalytic magnesium ions in the active center of the enzyme. However, DKAs display noncompetitive mode of inhibition with respect to NTP substrate, which contradicts the proposed mechanism. We have examined...
Article
Full-text available
It is supposed that alpha,gamma-diketo acids (DKAs) inhibit the activity of hepatitis C virus RNA-dependent RNA polymerase (RdRP HCV) via chelation of catalytic magnesium ions in the active center of the enzyme. However, DKAs display noncompetitive mode of inhibition with respect to NTP substrate, which contradicts the proposed mechanism. We have e...
Article
Bacterial pentaheme cytochrome c nitrite reductases (NrfAs) are key enzymes involved in the terminal step of dissimilatory nitrite reduction of the nitrogen cycle. Their structure and functions are well studied. Recently, a novel octaheme cytochrome c nitrite reductase (TvNiR) has been isolated from the haloalkaliphilic bacterium Thioalkalivibrio n...
Article
Full-text available
Substrate specificity of E. coli thymidine phosphorylase to pyrimidine nucleoside modified at 5'-, 3'-, and 2'-positions of sugar moiety has been studied. Equilibrium (K(eq)) and kinetics constants of phosphorolysis reaction of nucleosides were measured. The most important hydrogen bonds in enzyme-substrate complex have been determined.
Article
A new procedure for isolation of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens increasing significantly the yield of the purified enzyme is presented. The enzyme is isolated from the soluble fraction of the cell extract as a hexamer, as shown by gel filtration chromatography and small angle X-ra...
Article
Full-text available
Substrate specificity of Escherichia coli thymidine phosphorylase to thymidine derivatives modified at 5′-, 3′-, and 2′,3′-positions of the sugar moiety was studied. Equilibrium and kinetic constants (K m, K I, k cat) of the phosphorolysis reaction have been determined for 20 thymidine analogs. The results are compared with X-ray and molecular dyna...
Article
Full-text available
Pyrogallol reversibly and noncompetitively inhibits the activity of the hepatitis C RNA-dependent RNA polymerase. Based on molecular modeling of the inhibitor binding in the active site of the enzyme, the inhibition was suggested to be realized via chelation of two magnesium cations involved in the catalysis at the stage of the phosphoryl residue t...
Article
Full-text available
Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI2 with the coupled reduction of nicotinamide adenine dinucleotide (NAD+). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD+-azide complex) of FDH have been established earlier...
Article
A highly active cytochrome c nitrite reductase from the haloalkaliphilic sulfur-oxidizing non-ammonifying bacterium Tv. nitratireducens strain ALEN 2 (TvNiR) was isolated and purified to apparent electrophoretic homogeneity. The enzyme catalyzes reductive conversion of nitrite and hydroxylamine to ammonia without release of any intermediates, as we...
Article
Full-text available
A novel cytochrome c nitrite reductase (TvNiR) was isolated from the haloalkalophilic bacterium Thioalkalivibrio nitratireducens. The enzyme catalyses nitrite and hydroxylamine reduction, with ammonia as the only product of both reactions. It consists of 525 amino-acid residues and contains eight haems c. TvNiR crystals were grown by the hanging-dr...
Article
Full-text available
Formate dehydrogenase (FDG) from methylotrophic bacteria Pseudomonas sp. 101 catalyzes the reaction of oxidation of the formate ion to carbon dioxide, which is accompanied by the reduction of nicotinamid adenine dinucleotide (NAD+). The structures of the apo and holo (enzyme-NAD-azide triple complex) forms of the enzyme were determined earlier. In...
Article
Glutamate decarboxylase (GAD) is a pyridoxal enzyme that catalyzes the conversion of L-glutamate into gamma-aminobutyric acid and carbon dioxide. The Escherichia coli enzyme exists as two isozymes, referred to as GADalpha and GADbeta. Crystals of the complex of the recombinant isozyme GADalpha with glutarate as a substrate analogue were grown in sp...
Article
Crystals of Saccharomyces cerevisiae inorganic pyrophosphatase suitable for X-ray diffraction study were grown by cocrystallization of the enzyme with cobalt chloride and imidodiphosphate. Saccharomyces cerevisiae is a metal-dependent enzyme which catalyzes hydrolysis of inorganic pyrophosphate to orthophosphate. The three-dimensional structure of...
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.
Chapter
Summary This document is part of Subvolume A ‘Structural and Physical Data I’ of Volume 2 ‘Proteins - Biochemical and Physical Properties’ of Landolt-Börnstein - Group VII Biophysics.