Structural and mutational studies on substrate specificity and catalysis of Salmonella typhimurium D-cysteine desulfhydrase

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Bharath, Sakshibeedu R ^a   Bisht, Shveta ^a   Harijan, Rajesh K ^a   Savithri, Handanahal S ^a   Murthy, Mathur R N ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

1 AMINO A CARBOXY CYCLOPROPANE; 3 CHLORO DEXTRO ALANINE; ALANINE DERIVATIVE; CYCLOPROPANE DERIVATIVE; CYCLOSERINE; CYSTATHIONINE GAMMA LYASE; DEXTRO SERINE; LIGAND; POLYPEPTIDE; PYRIDOXAL 5 PHOSPHATE; PYRIDOXAMINE PHOSPHATE; PYRUVIC ACID; SERINE; TYROSINE; UNCLASSIFIED DRUG; 1 AMINOCYCLOPROPANECARBOXYLIC ACID; 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID; 3 CHLOROALANINE; 3-CHLOROALANINE; AMINO ACID; BETA ALANINE; DRUG DERIVATIVE;

ARTICLE; CATALYSIS; CHEMICAL BINDING; CHEMICAL REACTION; CONTROLLED STUDY; CRYSTAL; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME DEGRADATION; ENZYME INACTIVATION; ENZYME SPECIFICITY; MUTATIONAL ANALYSIS; PROTEIN DOMAIN; SALMONELLA TYPHIMURIUM; SPECTROSCOPY; STRUCTURE ANALYSIS; TRANSAMINATION; X RAY ANALYSIS; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; X RAY CRYSTALLOGRAPHY;

SALMONELLA TYPHIMURIUM;

AMINO ACIDS, CYCLIC; BETA-ALANINE; BIOCATALYSIS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; CYCLOSERINE; CYSTATHIONINE GAMMA-LYASE; DNA MUTATIONAL ANALYSIS; LIGANDS; MODELS, MOLECULAR; PYRIDOXAL PHOSPHATE; SALMONELLA TYPHIMURIUM; SUBSTRATE SPECIFICITY;

EID: 84860530513     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036267     Document Type: Article

References (39)

1. Toney MD, (2005) Reaction specificity in pyridoxal phosphate enzymes. Arch Biochem Biophys 433: 279-287.
2. Alexander FW, Sandmeier E, Mehta PK, Christen P, (1994) Evolutionary relationships among pyridoxal-5′-phosphate-dependent enzymes. Regio-specific alpha, beta and gamma families. Eur J Biochem 219: 953-960.
3. Jansonius JN, (1998) Structure, evolution and action of vitamin B6-dependent enzymes. Curr Opin Struct Biol 8: 759-769.
4. Bharath SR, Bisht S, Savithri HS, Murthy MR, (2011) Crystal structures of open and closed forms of d-serine deaminase from Salmonella typhimurium- implications on substrate specificity and catalysis. FEBS J 278: 2879-2891.
5. Inouye S, Goi H, Watanabe T, Hara T, Miyauchi K, et al. (1984) In vitro and in vivo antibacterial activities of MT-141, a new semisynthetic cephamycin, compared with those of five cephalosporins. Antimicrob Agents Chemother 26: 722-729.
6. Inouye S, Tsuruoka T, Goi H, Iwamatsu K, Miyauchi K, et al. (1984) Structure-activity relationships on the terminal D-amino acid moiety of a novel cephamycin MT-141. J Antibiot (Tokyo) 37: 1403-1413.
7. Nagasawa T, Ishii T, Kumagai H, Yamada H, (1985) D-Cysteine desulfhydrase of Escherichia coli. Purification and characterization. Eur J Biochem 153: 541-551.
8. Gallagher DT, Gilliland GL, Xiao G, Zondlo J, Fisher KE, et al. (1998) Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase. Structure 6: 465-475.
9. Yamada T, Komoto J, Takata Y, Ogawa H, Pitot HC, et al. (2003) Crystal structure of serine dehydratase from rat liver. Biochemistry 42: 12854-12865.
10. Simanshu DK, Savithri HS, Murthy MR, (2006) Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation. J Biol Chem 281: 39630-39641.
11. Grabowski R, Hofmeister AE, Buckel W, (1993) Bacterial L-serine dehydratases: a new family of enzymes containing iron-sulfur clusters. Trends Biochem Sci 18: 297-300.
12. Yao M, Ose T, Sugimoto H, Horiuchi A, Nakagawa A, et al. (2000) Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus. J Biol Chem 275: 34557-34565.
13. Karthikeyan S, Zhou Q, Zhao Z, Kao CL, Tao Z, et al. (2004) Structural analysis of Pseudomonas 1-aminocyclopropane-1-carboxylate deaminase complexes: insight into the mechanism of a unique pyridoxal-5′-phosphate dependent cyclopropane ring-opening reaction. Biochemistry 43: 13328-13339.
14. Fujino A, Ose T, Yao M, Tokiwano T, Honma M, et al. (2004) Structural and enzymatic properties of 1-aminocyclopropane-1-carboxylate deaminase homologue from Pyrococcus horikoshii. J Mol Biol 341: 999-1013.
15. Ose T, Fujino A, Yao M, Watanabe N, Honma M, et al. (2003) Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction. J Biol Chem 278: 41069-41076.
16. Ramachandran GN, Ramakrishnan C, Sasisekharan V, (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7: 95-99.
17. Lovell SC, Davis IW, Arendall WB III, de Bakker PI, Word JM, et al. (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50: 437-450.
18. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
19. Krissinel E, Henrick K, (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797.
20. Hyde CC, Ahmed SA, Padlan EA, Miles EW, Davies DR, (1988) Three-dimensional structure of the tryptophan synthase alpha 2 beta 2 multienzyme complex from Salmonella typhimurium. J Biol Chem 263: 17857-17871.
21. Burkhard P, Rao GS, Hohenester E, Schnackerz KD, Cook PF, et al. (1998) Three-dimensional structure of O-acetylserine sulfhydrylase from Salmonella typhimurium. J Mol Biol 283: 121-133.
22. Sharif S, Denisov GS, Toney MD, Limbach HH, (2007) NMR studies of coupled low- and high-barrier hydrogen bonds in pyridoxal-5′-phosphate model systems in polar solution. J Am Chem Soc 129: 6313-6327.
23. Todorovic B, Glick BR, (2008) The interconversion of ACC deaminase and D-cysteine desulfhydrase by directed mutagenesis. Planta 229: 193-205.
24. Petrek M, Otyepka M, Banas P, Kosinova P, Koca J, et al. (2006) CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 7: 316.
25. Pavelka A, Chovancova E, Damborsky J, (2009) HotSpot Wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Res 37: W376-383.
26. Federiuk CS, Shafer JA, (1983) A reaction pathway for transimination of the pyridoxal 5′-phosphate in D-serine dehydratase by amino acids. J Biol Chem 258: 5372-5378.
27. Ikushiro H, Hayashi H, Kagamiyama H, (2004) Reactions of serine palmitoyltransferase with serine and molecular mechanisms of the actions of serine derivatives as inhibitors. Biochemistry 43: 1082-1092.
28. Schnackerz KD, Ehrlich JH, Giesemann W, Reed TA, (1979) Mechanism of action of D-serine dehydratase. Identification of a transient intermediate. Biochemistry 18: 3557-3563.
29. Goto M, Yamauchi T, Kamiya N, Miyahara I, Yoshimura T, et al. (2009) Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe. J Biol Chem 284: 25944-25952.
30. Smith MA, Mack V, Ebneth A, Moraes I, Felicetti B, et al. (2010) The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding. J Biol Chem 285: 12873-12881.
31. Davis L, Metzler DE, (1972) pp. 33-74 The Enzymes: Academic press, New York.
32. Otwinowski Z, Minor W, (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods in Enzymology 276: 307-326.
33. CCP4, (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50: 760-763.
34. Cohen GE, (1997) ALIGN: a program to superimpose protein coordinates, accounting for insertions and deletions. Journal of Applied Crystallography 30: 1160-1161.
35. Krissinel E, Henrick K, (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60: 2256-2268.
36. Emsley P, Lohkamp B, Scott WG, Cowtan K, (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66: 486-501.
37. DeLano WL, (2002) The PyMOL Molecular Graphics System, DeLano Scientific LLC, San Carlos, CA.
38. Shenoy AR, Visweswariah SS, (2003) Site-directed mutagenesis using a single mutagenic oligonucleotide and DpnI digestion of template DNA. Anal Biochem 319: 335-336.
39. Ito T, Hemmi H, Kataoka K, Mukai Y, Yoshimura T, (2008) A novel zinc-dependent D-serine dehydratase from Saccharomyces cerevisiae. Biochem J 409: 399-406.