Svetlana Pakhomova - Academia.edu (original) (raw)
Papers by Svetlana Pakhomova
ChemInform, 1995
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Biochemistry, 2015
Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gr... more Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1'-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1'-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO2 from the carboxyphosphate intermediate to biotin.
Acta Crystallographica Section C Crystal Structure Communications, 1997
Biochemical and biophysical research communications, Jan 11, 2014
Dimethylglycine dehydrogenase (DMGDH) is a mammalian mitochondrial enzyme which plays an importan... more Dimethylglycine dehydrogenase (DMGDH) is a mammalian mitochondrial enzyme which plays an important role in the utilization of methyl groups derived from choline. DMGDH is a flavin containing enzyme which catalyzes the oxidative demethylation of dimethylglycine in vitro with the formation of sarcosine (N-methylglycine), hydrogen peroxide and formaldehyde. DMGDH binds tetrahydrofolate (THF) in vivo, which serves as an acceptor of formaldehyde and in the cell the product of the reaction is 5,10-methylenetetrahydrofolate instead of formaldehyde. To gain insight into the mechanism of the reaction we solved the crystal structures of the recombinant mature and precursor forms of rat DMGDH and DMGDH-THF complexes. Both forms of DMGDH reveal similar kinetic parameters and have the same tertiary structure fold with two domains formed by N- and C-terminal halves of the protein. The active center is located in the N-terminal domain while the THF binding site is located in the C-terminal domain ...
Protein science : a publication of the Protein Society, 2005
The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotrans... more The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotransferase superfamily, in complexes with the inactive form of the cofactor PAP 3'-phosphoadenosine 5'-phosphate (PAP) and (1) the product of the reaction with retinol anhydroretinol (AR), (2) the retinoid inhibitor all-trans-4-oxoretinol (OR), and (3) the potent steroid inhibitor androsterone (AND) have been determined and compared to the enzyme complex with PAP and retinol. The structures show that the geometry of the active-site amino acids is largely preserved in the various complexes. However, the beta-ionone rings of the retinoids are oriented differently with respect to side chains that have been shown to be important for the enzymatic reaction. In addition, the DHR:PAP:AND complex reveals a novel mode for steroid binding that contrasts significantly with that for steroid binding in other sulfotransferases. The molecule is displaced and rotated approximately 180 degrees along ...
Fresenius' Journal of Analytical Chemistry, 2001
The determination of iron(II) with 1,10-phenanthroline in aqueous solutions was carried out exemp... more The determination of iron(II) with 1,10-phenanthroline in aqueous solutions was carried out exemplarily by thermal lens spectrometry. The peculiarities of analytical reactions at the nanogram level of reactants can be studied using this method. Under the conditions of the competing reaction of ligand protonation, the overall stability constant for iron(II) chelate with 1,10-phenanthroline was determined at a level of n × 10 -7 mol L -1 , logβ 3 = 21.3 ± 0.1. The rates of formation and dissociation of iron(II) tris-(1,10-phenanthrolinate) at a level of n × 10 -8 mol L -1 were found to be (2.05 ± 0.05) × 10 -2 min -1 and (3.0 ± 0.1) × 10 -3 min -1 , respectively. The conditions for the determination of iron(II) with 1,10-phenanthroline by thermal lensing were reconsidered, and ascorbic acid was shown to be the best reducing agent, which provided minimum and reproducible sample pretreatment. Changes in the conditions at the nanogram level improved both the selectivity and sensitivity of determination. The optimum measurement conditions for thermal lensing were determined not only by the absorption of the analyte and reagents, but also by the background absorption of the solvent. The limits of detection and quantification of iron(II) at 488.0 nm (excitation beam power 140 mW) are 1 × 10 -9 and 6 × 10 -9 mol L -1 , respectively; the reproducibility RSD for the range n × 10 -8 -n × 10 -6 mol L -1 is 2-5%. Fresenius J Anal Chem (2001) 369 : 535-542
Present in the seawater dissolved oxygen is a key element that determines the balance of oxidants... more Present in the seawater dissolved oxygen is a key element that determines the balance of oxidants and reductants in the redox-layer of the Black Sea. Meanwhile, the accuracy and detection limit of the oxygen technique is an acute problem for studying the processes that occur in the redox zone. It became possible to significantly increase the accuracy of measurements of
Investigations of the redox-interfaces structure were performed in the NE Black Sea (central and ... more Investigations of the redox-interfaces structure were performed in the NE Black Sea (central and coastal parts) and Norwegian fjords (Bunnefjorden, Baerumsbassenget, Hunnbunn) in 2008-2009. Bunnefjorden is a 160 m deep anoxic basin, with flushing ones per several years, redox interface at about 90 m (aphotic zone); Baerumsbassenget is a 33 m deep permanent anoxic basin with redox interface positioned in
... Ladislav Cvak,B Alexandr Jegorov,*rb Petr Sedmera,c Vladimir HavliCek,c Jan OndraCek/ Michal ... more ... Ladislav Cvak,B Alexandr Jegorov,*rb Petr Sedmera,c Vladimir HavliCek,c Jan OndraCek/ Michal HuSak,d Svetlana Pakhomova,d Bohumil Kratochvil and Joachim Granzin a Galena Co., R. & D., 747 70 Opava-Komarov, Czech Republic Galena Co., Research Unit, Braniiovska ...
Collection of Czechoslovak Chemical Communications, 1994
... Alexandr JEGOROV a, Roman SOBOTIK b, Svetlana PAKHOMOVA c, Jan ONDRACEK c, Jiri NOVOTNY c, Mi... more ... Alexandr JEGOROV a, Roman SOBOTIK b, Svetlana PAKHOMOVA c, Jan ONDRACEK c, Jiri NOVOTNY c, Michal HUSAK c and Bohumil KRATOCHVIL c a Galena Co., Research Unit, 370 05 Ceske Budejovice, The Czech Republic b Galena Co., R.& D., 747 70 Opava ...
Tetrahedron Letters, 1998
... a Department of Organic Chemistry, Institute of Chemical Technology, Technicka´5, Prague 6, C... more ... a Department of Organic Chemistry, Institute of Chemical Technology, Technicka´5, Prague 6, Czech republic. b Department of Solid State Chemistry, Institute of Chemical Technology, Technicka´5, Prague 6, Czech republic. ...
Oceanology, 2006
Without Abstract
Oceanology, 2009
During the cruises of the R/V Knorr in 2003 and the R/V Akvanavt in 2004–2006, the vertical distr... more During the cruises of the R/V Knorr in 2003 and the R/V Akvanavt in 2004–2006, the vertical distribution of the dissolved and particulate forms of iron and manganese in the redox zone was studied in the southwestern and northeastern parts of the Black Sea. The temporal and spatial variations in the distribution of studied elements were shown.
Oceanology, 2007
ABSTRACT no abstract
Proteins: Structure, Function, and Bioinformatics, 2004
Glycine N-methyltransferases (GNMTs) from three mammalian sources were compared with respect to t... more Glycine N-methyltransferases (GNMTs) from three mammalian sources were compared with respect to their crystal structures and kinetic parameters. The crystal structure for the rat enzyme was published previously. Human and mouse GNMT were expressed in Escherichia coli in order to determine their crystal structures. Mouse GNMT was crystallized in two crystal forms, a monoclinic form and a tetragonal form. Comparison of the three structures reveals subtle differences, which may relate to the different kinetic properties of the enzymes. The flexible character of several loops surrounding the active site, along with an analysis of the active site boundaries, indicates that the observed conformations of human and mouse GNMTs are more open than that of the rat enzyme. There is an increase in kcat when going from rat to mouse to human, suggesting a correlation with the increased flexibility of some structural elements of the respective enzymes.
Protein Science, 2007
In the presence of moderate (2-4 M) urea concentrations the tetrameric enzyme, glycine N-methyltr... more In the presence of moderate (2-4 M) urea concentrations the tetrameric enzyme, glycine N-methyltransferase (GNMT), dissociates into compact monomers. Higher concentrations of urea (7-8 M) promote complete denaturation of the enzyme. We report here that the H176N mutation in this enzyme, found in humans with hypermethioninaemia, significantly decreases stability of the tetramer, although H176 is located far from the intersubunit contact areas. Dissociation of the tetramer to compact monomers and unfolding of compact monomers of the mutant protein were detected by circular dichroism, quenching of fluorescence emission, size-exclusion chromatography, and enzyme activity. The values of apparent free energy of dissociation of tetramer and of unfolding of compact monomers for the H176N mutant (27.7 and 4.2 kcal/mol, respectively) are lower than those of wild-type protein (37.5 and 6.2 kcal/mol). A 2.7 Å resolution structure of the mutant protein revealed no significant difference in the conformation of the protein near the mutated residue.
Protein Science, 2004
The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been estab... more The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been established at a resolution of 2.5 Å. The protein crystallized without bound Mn(II) and K + , ions crucial for efficient catalysis, providing a structure of the apo enzyme. The protein maintains the three-dimensional domainswapped arrangement of the paired ␣-motifs observed in the genomically encoded homologous enzyme from Pseudomonas aeruginosa (PA1129). The basic architecture of the active site is also maintained, despite the absence of the catalytically essential Mn(II). However, the absence of K + , which has been shown to enhance enzymatic activity, appears to contribute to conformational heterogeneity in the K +binding loops.
Protein Science, 2009
True catalases are tyrosine-liganded, usually tetrameric, hemoproteins with subunit sizes of appr... more True catalases are tyrosine-liganded, usually tetrameric, hemoproteins with subunit sizes of approximately 55-84 kDa. Recently characterized hemoproteins with a catalase-related structure, yet lacking in catalatic activity, include the 40-43 kDa allene oxide synthases of marine invertebrates and cyanobacteria. Herein, we describe the 1.8 A X-ray crystal structure of a 33 kDa subunit hemoprotein from Mycobacterium avium ssp. paratuberculosis (annotated as MAP-2744c), that retains the core elements of the catalase fold and exhibits an organic peroxide-dependent peroxidase activity. MAP-2744c exhibits negligible catalatic activity, weak peroxidatic activity using hydrogen peroxide (20/s) and strong peroxidase activity (approximately 300/s) using organic hydroperoxides as co-substrate. Key amino acid differences significantly impact prosthetic group conformation and placement and confer a distinct activity to this prototypical member of a group of conserved bacterial "minicatalases". Its structural features and the result of the enzyme assays support a role for MAP-2744c and its close homologues in mitigating challenge by a variety of reactive oxygen species.
ChemInform, 1995
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Biochemistry, 2015
Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gr... more Acetyl-CoA carboxylase catalyzes the first and regulated step in fatty acid synthesis. In most Gram-negative and Gram-positive bacteria, the enzyme is composed of three proteins: biotin carboxylase, a biotin carboxyl carrier protein (BCCP), and carboxyltransferase. The reaction mechanism involves two half-reactions with biotin carboxylase catalyzing the ATP-dependent carboxylation of biotin-BCCP in the first reaction. In the second reaction, carboxyltransferase catalyzes the transfer of the carboxyl group from biotin-BCCP to acetyl-CoA to form malonyl-CoA. In this report, high-resolution crystal structures of biotin carboxylase from Haemophilus influenzae were determined with bicarbonate, the ATP analogue AMPPCP; the carboxyphosphate intermediate analogues, phosphonoacetamide and phosphonoformate; the products ADP and phosphate; and the carboxybiotin analogue N1'-methoxycarbonyl biotin methyl ester. The structures have a common theme in that bicarbonate, phosphate, and the methyl ester of the carboxyl group of N1'-methoxycarbonyl biotin methyl ester all bound in the same pocket in the active site of biotin carboxylase and as such utilize the same set of amino acids for binding. This finding suggests a catalytic mechanism for biotin carboxylase in which the binding pocket that binds tetrahedral phosphate also accommodates and stabilizes a tetrahedral dianionic transition state resulting from direct transfer of CO2 from the carboxyphosphate intermediate to biotin.
Acta Crystallographica Section C Crystal Structure Communications, 1997
Biochemical and biophysical research communications, Jan 11, 2014
Dimethylglycine dehydrogenase (DMGDH) is a mammalian mitochondrial enzyme which plays an importan... more Dimethylglycine dehydrogenase (DMGDH) is a mammalian mitochondrial enzyme which plays an important role in the utilization of methyl groups derived from choline. DMGDH is a flavin containing enzyme which catalyzes the oxidative demethylation of dimethylglycine in vitro with the formation of sarcosine (N-methylglycine), hydrogen peroxide and formaldehyde. DMGDH binds tetrahydrofolate (THF) in vivo, which serves as an acceptor of formaldehyde and in the cell the product of the reaction is 5,10-methylenetetrahydrofolate instead of formaldehyde. To gain insight into the mechanism of the reaction we solved the crystal structures of the recombinant mature and precursor forms of rat DMGDH and DMGDH-THF complexes. Both forms of DMGDH reveal similar kinetic parameters and have the same tertiary structure fold with two domains formed by N- and C-terminal halves of the protein. The active center is located in the N-terminal domain while the THF binding site is located in the C-terminal domain ...
Protein science : a publication of the Protein Society, 2005
The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotrans... more The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotransferase superfamily, in complexes with the inactive form of the cofactor PAP 3'-phosphoadenosine 5'-phosphate (PAP) and (1) the product of the reaction with retinol anhydroretinol (AR), (2) the retinoid inhibitor all-trans-4-oxoretinol (OR), and (3) the potent steroid inhibitor androsterone (AND) have been determined and compared to the enzyme complex with PAP and retinol. The structures show that the geometry of the active-site amino acids is largely preserved in the various complexes. However, the beta-ionone rings of the retinoids are oriented differently with respect to side chains that have been shown to be important for the enzymatic reaction. In addition, the DHR:PAP:AND complex reveals a novel mode for steroid binding that contrasts significantly with that for steroid binding in other sulfotransferases. The molecule is displaced and rotated approximately 180 degrees along ...
Fresenius' Journal of Analytical Chemistry, 2001
The determination of iron(II) with 1,10-phenanthroline in aqueous solutions was carried out exemp... more The determination of iron(II) with 1,10-phenanthroline in aqueous solutions was carried out exemplarily by thermal lens spectrometry. The peculiarities of analytical reactions at the nanogram level of reactants can be studied using this method. Under the conditions of the competing reaction of ligand protonation, the overall stability constant for iron(II) chelate with 1,10-phenanthroline was determined at a level of n × 10 -7 mol L -1 , logβ 3 = 21.3 ± 0.1. The rates of formation and dissociation of iron(II) tris-(1,10-phenanthrolinate) at a level of n × 10 -8 mol L -1 were found to be (2.05 ± 0.05) × 10 -2 min -1 and (3.0 ± 0.1) × 10 -3 min -1 , respectively. The conditions for the determination of iron(II) with 1,10-phenanthroline by thermal lensing were reconsidered, and ascorbic acid was shown to be the best reducing agent, which provided minimum and reproducible sample pretreatment. Changes in the conditions at the nanogram level improved both the selectivity and sensitivity of determination. The optimum measurement conditions for thermal lensing were determined not only by the absorption of the analyte and reagents, but also by the background absorption of the solvent. The limits of detection and quantification of iron(II) at 488.0 nm (excitation beam power 140 mW) are 1 × 10 -9 and 6 × 10 -9 mol L -1 , respectively; the reproducibility RSD for the range n × 10 -8 -n × 10 -6 mol L -1 is 2-5%. Fresenius J Anal Chem (2001) 369 : 535-542
Present in the seawater dissolved oxygen is a key element that determines the balance of oxidants... more Present in the seawater dissolved oxygen is a key element that determines the balance of oxidants and reductants in the redox-layer of the Black Sea. Meanwhile, the accuracy and detection limit of the oxygen technique is an acute problem for studying the processes that occur in the redox zone. It became possible to significantly increase the accuracy of measurements of
Investigations of the redox-interfaces structure were performed in the NE Black Sea (central and ... more Investigations of the redox-interfaces structure were performed in the NE Black Sea (central and coastal parts) and Norwegian fjords (Bunnefjorden, Baerumsbassenget, Hunnbunn) in 2008-2009. Bunnefjorden is a 160 m deep anoxic basin, with flushing ones per several years, redox interface at about 90 m (aphotic zone); Baerumsbassenget is a 33 m deep permanent anoxic basin with redox interface positioned in
... Ladislav Cvak,B Alexandr Jegorov,*rb Petr Sedmera,c Vladimir HavliCek,c Jan OndraCek/ Michal ... more ... Ladislav Cvak,B Alexandr Jegorov,*rb Petr Sedmera,c Vladimir HavliCek,c Jan OndraCek/ Michal HuSak,d Svetlana Pakhomova,d Bohumil Kratochvil and Joachim Granzin a Galena Co., R. & D., 747 70 Opava-Komarov, Czech Republic Galena Co., Research Unit, Braniiovska ...
Collection of Czechoslovak Chemical Communications, 1994
... Alexandr JEGOROV a, Roman SOBOTIK b, Svetlana PAKHOMOVA c, Jan ONDRACEK c, Jiri NOVOTNY c, Mi... more ... Alexandr JEGOROV a, Roman SOBOTIK b, Svetlana PAKHOMOVA c, Jan ONDRACEK c, Jiri NOVOTNY c, Michal HUSAK c and Bohumil KRATOCHVIL c a Galena Co., Research Unit, 370 05 Ceske Budejovice, The Czech Republic b Galena Co., R.& D., 747 70 Opava ...
Tetrahedron Letters, 1998
... a Department of Organic Chemistry, Institute of Chemical Technology, Technicka´5, Prague 6, C... more ... a Department of Organic Chemistry, Institute of Chemical Technology, Technicka´5, Prague 6, Czech republic. b Department of Solid State Chemistry, Institute of Chemical Technology, Technicka´5, Prague 6, Czech republic. ...
Oceanology, 2006
Without Abstract
Oceanology, 2009
During the cruises of the R/V Knorr in 2003 and the R/V Akvanavt in 2004–2006, the vertical distr... more During the cruises of the R/V Knorr in 2003 and the R/V Akvanavt in 2004–2006, the vertical distribution of the dissolved and particulate forms of iron and manganese in the redox zone was studied in the southwestern and northeastern parts of the Black Sea. The temporal and spatial variations in the distribution of studied elements were shown.
Oceanology, 2007
ABSTRACT no abstract
Proteins: Structure, Function, and Bioinformatics, 2004
Glycine N-methyltransferases (GNMTs) from three mammalian sources were compared with respect to t... more Glycine N-methyltransferases (GNMTs) from three mammalian sources were compared with respect to their crystal structures and kinetic parameters. The crystal structure for the rat enzyme was published previously. Human and mouse GNMT were expressed in Escherichia coli in order to determine their crystal structures. Mouse GNMT was crystallized in two crystal forms, a monoclinic form and a tetragonal form. Comparison of the three structures reveals subtle differences, which may relate to the different kinetic properties of the enzymes. The flexible character of several loops surrounding the active site, along with an analysis of the active site boundaries, indicates that the observed conformations of human and mouse GNMTs are more open than that of the rat enzyme. There is an increase in kcat when going from rat to mouse to human, suggesting a correlation with the increased flexibility of some structural elements of the respective enzymes.
Protein Science, 2007
In the presence of moderate (2-4 M) urea concentrations the tetrameric enzyme, glycine N-methyltr... more In the presence of moderate (2-4 M) urea concentrations the tetrameric enzyme, glycine N-methyltransferase (GNMT), dissociates into compact monomers. Higher concentrations of urea (7-8 M) promote complete denaturation of the enzyme. We report here that the H176N mutation in this enzyme, found in humans with hypermethioninaemia, significantly decreases stability of the tetramer, although H176 is located far from the intersubunit contact areas. Dissociation of the tetramer to compact monomers and unfolding of compact monomers of the mutant protein were detected by circular dichroism, quenching of fluorescence emission, size-exclusion chromatography, and enzyme activity. The values of apparent free energy of dissociation of tetramer and of unfolding of compact monomers for the H176N mutant (27.7 and 4.2 kcal/mol, respectively) are lower than those of wild-type protein (37.5 and 6.2 kcal/mol). A 2.7 Å resolution structure of the mutant protein revealed no significant difference in the conformation of the protein near the mutated residue.
Protein Science, 2004
The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been estab... more The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been established at a resolution of 2.5 Å. The protein crystallized without bound Mn(II) and K + , ions crucial for efficient catalysis, providing a structure of the apo enzyme. The protein maintains the three-dimensional domainswapped arrangement of the paired ␣-motifs observed in the genomically encoded homologous enzyme from Pseudomonas aeruginosa (PA1129). The basic architecture of the active site is also maintained, despite the absence of the catalytically essential Mn(II). However, the absence of K + , which has been shown to enhance enzymatic activity, appears to contribute to conformational heterogeneity in the K +binding loops.
Protein Science, 2009
True catalases are tyrosine-liganded, usually tetrameric, hemoproteins with subunit sizes of appr... more True catalases are tyrosine-liganded, usually tetrameric, hemoproteins with subunit sizes of approximately 55-84 kDa. Recently characterized hemoproteins with a catalase-related structure, yet lacking in catalatic activity, include the 40-43 kDa allene oxide synthases of marine invertebrates and cyanobacteria. Herein, we describe the 1.8 A X-ray crystal structure of a 33 kDa subunit hemoprotein from Mycobacterium avium ssp. paratuberculosis (annotated as MAP-2744c), that retains the core elements of the catalase fold and exhibits an organic peroxide-dependent peroxidase activity. MAP-2744c exhibits negligible catalatic activity, weak peroxidatic activity using hydrogen peroxide (20/s) and strong peroxidase activity (approximately 300/s) using organic hydroperoxides as co-substrate. Key amino acid differences significantly impact prosthetic group conformation and placement and confer a distinct activity to this prototypical member of a group of conserved bacterial "minicatalases". Its structural features and the result of the enzyme assays support a role for MAP-2744c and its close homologues in mitigating challenge by a variety of reactive oxygen species.