Structure, mechanism, and conformational dynamics of O-acetylserine sulfhydrylase from Salmonella typhimurium: Comparison of A and B isozymes

Arundhati Chattopadhyay, Markus Meier, Sergei Ivaninskii, Peter Burkhard, Francesca Speroni, Barbara Campanini, Stefano Bettati, Andrea Mozzarelli, Wael Rabeh, Lei Li, Paul F. Cook

Research output: Contribution to journalArticle

Abstract

O-Acetylserine sulfhydrylase is a pyridoxal 5′-phosphate-dependent enzyme that catalyzes the final step in the cysteine biosynthetic pathway in enteric bacteria and plants, the replacement of the β-acetoxy group of O-acetyl-L-serine by a thiol to give L-cysteine. Two isozymes are found in Salmonella typhimurium, with the A-isozyme expressed under aerobic and the B-isozyme expressed under anaerobic conditions. The structure of O-acetylserine sulfhydrylase B has been solved to 2.3 Å and exhibits overall a fold very similar to that of the A-isozyme. The main difference between the two isozymes is the more hydrophilic active site of the B-isozyme with two ionizable residues, C280 and D281, replacing the neutral residues S300 and P299, respectively, in the A-isozyme. D281 is above the re face of the cofactor and is within hydrogen-bonding distance to Y286, while C280 is located about 3.4 Å from the pyridine nitrogen (N1) of the internal Schiff base. The B-isozyme has a turnover number (V/Et) 12.5-fold higher than the A-isozyme and an ∼10-fold lower Km for O-acetyl-L-serine. Studies of the first half-reaction by rapid-scanning stopped-flow indicate a first-order conversion of the internal Schiff base to the α-aminoacrylate intermediate at any concentration of O-acetyl-L-serine. The Kd values for formation of the external Schiff base with cysteine and serine, obtained by spectral titration, are pH dependent and exhibit a pKa of 7.0-7.5 (for a group that must be unprotonated for optimum binding) with values, above pH 8.0, of about 3.0 and 30.0 mM, respectively. In both cases the neutral enolimine is favored at high pH. Failure to observe the pKa for the α-amines of cysteine and serine in the pKESB vs pH profile suggests a compensatory effect resulting from titration of a group on the enzyme with a pKa in the vicinity of the α-amine's pKa. The pH dependence of the first-order rate constant for decay of the α-aminoacrylate intermediate to give pyruvate and ammonia gives a pK a of about 9 for the active site lysine (K41), a pH unit higher than that of the A-isozyme. The difference in pH dependence of the pKESB for cysteine and serine, the higher pKa for K41, and the preference for the neutral species at high pH compared to the A-isozyme can be explained by titration of C280 to give the thiolate. Subtle conformational differences between O-acetylserine sulfhydrylase A and O-acetylserine sulfhydrylase B are detected by comparing the absorption and emission spectra of the internal aldimine in the absence and presence of the product acetate and of the external aldimine with L-serine. The two isozymes show a different equilibrium distribution of the enolimine and ketoenamine tautomers, likely as a result of a more polar active site for O-acetylserine sulfhydrylase B. The distribution of cofactor tautomers is dramatically affected by the ligation state of the enzyme. In the presence of acetate, which occupies the α-carboxylate subsite, the equilibrium between tautomers is shifted toward the ketoenamine tautomer, as a result of a conformational change affecting the structure of the active site. This finding, in agreement with structural data, suggests for the O-acetylserine sulfhydrylase B-isozyme a higher degree of conformational flexibility linked to catalysis.

Original languageEnglish (US)
Pages (from-to)8315-8330
Number of pages16
JournalBiochemistry
Volume46
Issue number28
DOIs
StatePublished - Jul 17 2007

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Cysteine Synthase
Salmonella
Salmonella typhimurium
Isoenzymes
Serine
Cysteine
Schiff Bases
Catalytic Domain
Titration
Amines
Acetates
Enzymes
Pyridoxal Phosphate
Biosynthetic Pathways
Enterobacteriaceae
Hydrogen Bonding

ASJC Scopus subject areas

  • Biochemistry

Cite this

Chattopadhyay, A., Meier, M., Ivaninskii, S., Burkhard, P., Speroni, F., Campanini, B., ... Cook, P. F. (2007). Structure, mechanism, and conformational dynamics of O-acetylserine sulfhydrylase from Salmonella typhimurium: Comparison of A and B isozymes. Biochemistry, 46(28), 8315-8330. https://doi.org/10.1021/bi602603c

Structure, mechanism, and conformational dynamics of O-acetylserine sulfhydrylase from Salmonella typhimurium : Comparison of A and B isozymes. / Chattopadhyay, Arundhati; Meier, Markus; Ivaninskii, Sergei; Burkhard, Peter; Speroni, Francesca; Campanini, Barbara; Bettati, Stefano; Mozzarelli, Andrea; Rabeh, Wael; Li, Lei; Cook, Paul F.

In: Biochemistry, Vol. 46, No. 28, 17.07.2007, p. 8315-8330.

Research output: Contribution to journalArticle

Chattopadhyay, A, Meier, M, Ivaninskii, S, Burkhard, P, Speroni, F, Campanini, B, Bettati, S, Mozzarelli, A, Rabeh, W, Li, L & Cook, PF 2007, 'Structure, mechanism, and conformational dynamics of O-acetylserine sulfhydrylase from Salmonella typhimurium: Comparison of A and B isozymes', Biochemistry, vol. 46, no. 28, pp. 8315-8330. https://doi.org/10.1021/bi602603c
Chattopadhyay, Arundhati ; Meier, Markus ; Ivaninskii, Sergei ; Burkhard, Peter ; Speroni, Francesca ; Campanini, Barbara ; Bettati, Stefano ; Mozzarelli, Andrea ; Rabeh, Wael ; Li, Lei ; Cook, Paul F. / Structure, mechanism, and conformational dynamics of O-acetylserine sulfhydrylase from Salmonella typhimurium : Comparison of A and B isozymes. In: Biochemistry. 2007 ; Vol. 46, No. 28. pp. 8315-8330.
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abstract = "O-Acetylserine sulfhydrylase is a pyridoxal 5′-phosphate-dependent enzyme that catalyzes the final step in the cysteine biosynthetic pathway in enteric bacteria and plants, the replacement of the β-acetoxy group of O-acetyl-L-serine by a thiol to give L-cysteine. Two isozymes are found in Salmonella typhimurium, with the A-isozyme expressed under aerobic and the B-isozyme expressed under anaerobic conditions. The structure of O-acetylserine sulfhydrylase B has been solved to 2.3 {\AA} and exhibits overall a fold very similar to that of the A-isozyme. The main difference between the two isozymes is the more hydrophilic active site of the B-isozyme with two ionizable residues, C280 and D281, replacing the neutral residues S300 and P299, respectively, in the A-isozyme. D281 is above the re face of the cofactor and is within hydrogen-bonding distance to Y286, while C280 is located about 3.4 {\AA} from the pyridine nitrogen (N1) of the internal Schiff base. The B-isozyme has a turnover number (V/Et) 12.5-fold higher than the A-isozyme and an ∼10-fold lower Km for O-acetyl-L-serine. Studies of the first half-reaction by rapid-scanning stopped-flow indicate a first-order conversion of the internal Schiff base to the α-aminoacrylate intermediate at any concentration of O-acetyl-L-serine. The Kd values for formation of the external Schiff base with cysteine and serine, obtained by spectral titration, are pH dependent and exhibit a pKa of 7.0-7.5 (for a group that must be unprotonated for optimum binding) with values, above pH 8.0, of about 3.0 and 30.0 mM, respectively. In both cases the neutral enolimine is favored at high pH. Failure to observe the pKa for the α-amines of cysteine and serine in the pKESB vs pH profile suggests a compensatory effect resulting from titration of a group on the enzyme with a pKa in the vicinity of the α-amine's pKa. The pH dependence of the first-order rate constant for decay of the α-aminoacrylate intermediate to give pyruvate and ammonia gives a pK a of about 9 for the active site lysine (K41), a pH unit higher than that of the A-isozyme. The difference in pH dependence of the pKESB for cysteine and serine, the higher pKa for K41, and the preference for the neutral species at high pH compared to the A-isozyme can be explained by titration of C280 to give the thiolate. Subtle conformational differences between O-acetylserine sulfhydrylase A and O-acetylserine sulfhydrylase B are detected by comparing the absorption and emission spectra of the internal aldimine in the absence and presence of the product acetate and of the external aldimine with L-serine. The two isozymes show a different equilibrium distribution of the enolimine and ketoenamine tautomers, likely as a result of a more polar active site for O-acetylserine sulfhydrylase B. The distribution of cofactor tautomers is dramatically affected by the ligation state of the enzyme. In the presence of acetate, which occupies the α-carboxylate subsite, the equilibrium between tautomers is shifted toward the ketoenamine tautomer, as a result of a conformational change affecting the structure of the active site. This finding, in agreement with structural data, suggests for the O-acetylserine sulfhydrylase B-isozyme a higher degree of conformational flexibility linked to catalysis.",
author = "Arundhati Chattopadhyay and Markus Meier and Sergei Ivaninskii and Peter Burkhard and Francesca Speroni and Barbara Campanini and Stefano Bettati and Andrea Mozzarelli and Wael Rabeh and Lei Li and Cook, {Paul F.}",
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T1 - Structure, mechanism, and conformational dynamics of O-acetylserine sulfhydrylase from Salmonella typhimurium

T2 - Comparison of A and B isozymes

AU - Chattopadhyay, Arundhati

AU - Meier, Markus

AU - Ivaninskii, Sergei

AU - Burkhard, Peter

AU - Speroni, Francesca

AU - Campanini, Barbara

AU - Bettati, Stefano

AU - Mozzarelli, Andrea

AU - Rabeh, Wael

AU - Li, Lei

AU - Cook, Paul F.

PY - 2007/7/17

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N2 - O-Acetylserine sulfhydrylase is a pyridoxal 5′-phosphate-dependent enzyme that catalyzes the final step in the cysteine biosynthetic pathway in enteric bacteria and plants, the replacement of the β-acetoxy group of O-acetyl-L-serine by a thiol to give L-cysteine. Two isozymes are found in Salmonella typhimurium, with the A-isozyme expressed under aerobic and the B-isozyme expressed under anaerobic conditions. The structure of O-acetylserine sulfhydrylase B has been solved to 2.3 Å and exhibits overall a fold very similar to that of the A-isozyme. The main difference between the two isozymes is the more hydrophilic active site of the B-isozyme with two ionizable residues, C280 and D281, replacing the neutral residues S300 and P299, respectively, in the A-isozyme. D281 is above the re face of the cofactor and is within hydrogen-bonding distance to Y286, while C280 is located about 3.4 Å from the pyridine nitrogen (N1) of the internal Schiff base. The B-isozyme has a turnover number (V/Et) 12.5-fold higher than the A-isozyme and an ∼10-fold lower Km for O-acetyl-L-serine. Studies of the first half-reaction by rapid-scanning stopped-flow indicate a first-order conversion of the internal Schiff base to the α-aminoacrylate intermediate at any concentration of O-acetyl-L-serine. The Kd values for formation of the external Schiff base with cysteine and serine, obtained by spectral titration, are pH dependent and exhibit a pKa of 7.0-7.5 (for a group that must be unprotonated for optimum binding) with values, above pH 8.0, of about 3.0 and 30.0 mM, respectively. In both cases the neutral enolimine is favored at high pH. Failure to observe the pKa for the α-amines of cysteine and serine in the pKESB vs pH profile suggests a compensatory effect resulting from titration of a group on the enzyme with a pKa in the vicinity of the α-amine's pKa. The pH dependence of the first-order rate constant for decay of the α-aminoacrylate intermediate to give pyruvate and ammonia gives a pK a of about 9 for the active site lysine (K41), a pH unit higher than that of the A-isozyme. The difference in pH dependence of the pKESB for cysteine and serine, the higher pKa for K41, and the preference for the neutral species at high pH compared to the A-isozyme can be explained by titration of C280 to give the thiolate. Subtle conformational differences between O-acetylserine sulfhydrylase A and O-acetylserine sulfhydrylase B are detected by comparing the absorption and emission spectra of the internal aldimine in the absence and presence of the product acetate and of the external aldimine with L-serine. The two isozymes show a different equilibrium distribution of the enolimine and ketoenamine tautomers, likely as a result of a more polar active site for O-acetylserine sulfhydrylase B. The distribution of cofactor tautomers is dramatically affected by the ligation state of the enzyme. In the presence of acetate, which occupies the α-carboxylate subsite, the equilibrium between tautomers is shifted toward the ketoenamine tautomer, as a result of a conformational change affecting the structure of the active site. This finding, in agreement with structural data, suggests for the O-acetylserine sulfhydrylase B-isozyme a higher degree of conformational flexibility linked to catalysis.

AB - O-Acetylserine sulfhydrylase is a pyridoxal 5′-phosphate-dependent enzyme that catalyzes the final step in the cysteine biosynthetic pathway in enteric bacteria and plants, the replacement of the β-acetoxy group of O-acetyl-L-serine by a thiol to give L-cysteine. Two isozymes are found in Salmonella typhimurium, with the A-isozyme expressed under aerobic and the B-isozyme expressed under anaerobic conditions. The structure of O-acetylserine sulfhydrylase B has been solved to 2.3 Å and exhibits overall a fold very similar to that of the A-isozyme. The main difference between the two isozymes is the more hydrophilic active site of the B-isozyme with two ionizable residues, C280 and D281, replacing the neutral residues S300 and P299, respectively, in the A-isozyme. D281 is above the re face of the cofactor and is within hydrogen-bonding distance to Y286, while C280 is located about 3.4 Å from the pyridine nitrogen (N1) of the internal Schiff base. The B-isozyme has a turnover number (V/Et) 12.5-fold higher than the A-isozyme and an ∼10-fold lower Km for O-acetyl-L-serine. Studies of the first half-reaction by rapid-scanning stopped-flow indicate a first-order conversion of the internal Schiff base to the α-aminoacrylate intermediate at any concentration of O-acetyl-L-serine. The Kd values for formation of the external Schiff base with cysteine and serine, obtained by spectral titration, are pH dependent and exhibit a pKa of 7.0-7.5 (for a group that must be unprotonated for optimum binding) with values, above pH 8.0, of about 3.0 and 30.0 mM, respectively. In both cases the neutral enolimine is favored at high pH. Failure to observe the pKa for the α-amines of cysteine and serine in the pKESB vs pH profile suggests a compensatory effect resulting from titration of a group on the enzyme with a pKa in the vicinity of the α-amine's pKa. The pH dependence of the first-order rate constant for decay of the α-aminoacrylate intermediate to give pyruvate and ammonia gives a pK a of about 9 for the active site lysine (K41), a pH unit higher than that of the A-isozyme. The difference in pH dependence of the pKESB for cysteine and serine, the higher pKa for K41, and the preference for the neutral species at high pH compared to the A-isozyme can be explained by titration of C280 to give the thiolate. Subtle conformational differences between O-acetylserine sulfhydrylase A and O-acetylserine sulfhydrylase B are detected by comparing the absorption and emission spectra of the internal aldimine in the absence and presence of the product acetate and of the external aldimine with L-serine. The two isozymes show a different equilibrium distribution of the enolimine and ketoenamine tautomers, likely as a result of a more polar active site for O-acetylserine sulfhydrylase B. The distribution of cofactor tautomers is dramatically affected by the ligation state of the enzyme. In the presence of acetate, which occupies the α-carboxylate subsite, the equilibrium between tautomers is shifted toward the ketoenamine tautomer, as a result of a conformational change affecting the structure of the active site. This finding, in agreement with structural data, suggests for the O-acetylserine sulfhydrylase B-isozyme a higher degree of conformational flexibility linked to catalysis.

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