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Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins.

Matsuda K, Mizuguchi K, Nishioka T, Kato H, Go N, Oda J
Protein Eng 9 1083-92 (1996)
Cited: 19 times
EuropePMC logo PMID: 9010922

Abstract

The crystal structure of Escherichia coli B glutathione synthetase (GSHase) has been determined at the optimal catalytic condition pH 7.5. The most significant structural difference from the structure at pH 6.0 is the movement of the central domain towards the N-terminal domain almost as a rigid body. As a result of this movement, new interdomain and intersubunit polar interactions are formed which stabilize the dimeric structure further. The structure of GSHase at optimal pH was compared with 294 other known protein structures in terms of the spatial arrangements of secondary structural elements. Three enzymes (D-alanine: D-alanine ligase, succinyl-CoA synthetase and the biotin carboxylase subunit of acetyl-CoA carboxylase) were found to have structures similar to the ATP-binding site of GSHase, which extends across two domains. The ATP-binding sites in these four enzymes are composed of two antiparallel beta-sheets and are different from the classic mononucleotide-binding fold. Except for these proteins, no significant structural similarity was detected between GSHase and the other ATP-binding proteins. A structural motif in the N-terminal domain of GSHase has been found to be similar to the NAD-binding fold. This structural motif is shared by a number of other proteins that bind various negatively charged molecules.

Reviews - 1gsh mentioned but not cited (1)

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Articles - 1gsh mentioned but not cited (3)

  1. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase. Kuhn D, Weskamp N, Schmitt S, Hüllermeier E, Klebe G. J Mol Biol 359 1023-1044 (2006)
  2. Molecular identification of N-acetylaspartylglutamate synthase and beta-citrylglutamate synthase. Collard F, Stroobant V, Lamosa P, Kapanda CN, Lambert DM, Muccioli GG, Poupaert JH, Opperdoes F, Van Schaftingen E. J Biol Chem 285 29826-29833 (2010)
  3. The eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications. Burroughs AM, Zhang D, Aravind L. Biol Direct 10 21 (2015)


Reviews citing this publication (1)

  1. Glutathione in bacteria. Smirnova GV, Oktyabrsky ON. Biochemistry (Mosc) 70 1199-1211 (2005)

Articles citing this publication (14)

  1. A diverse superfamily of enzymes with ATP-dependent carboxylate-amine/thiol ligase activity. Galperin MY, Koonin EV. Protein Sci 6 2639-2643 (1997)
  2. The geometry of domain combination in proteins. Bashton M, Chothia C. J Mol Biol 315 927-939 (2002)
  3. Synapsin I is structurally similar to ATP-utilizing enzymes. Esser L, Wang CR, Hosaka M, Smagula CS, Südhof TC, Deisenhofer J. EMBO J 17 977-984 (1998)
  4. When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Denessiouk KA, Johnson MS. Proteins 38 310-326 (2000)
  5. Structural and theoretical studies suggest domain movement produces an active conformation of thymidine phosphorylase. Pugmire MJ, Cook WJ, Jasanoff A, Walter MR, Ealick SE. J Mol Biol 281 285-299 (1998)
  6. The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis. Levdikov VM, Barynin VV, Grebenko AI, Melik-Adamyan WR, Lamzin VS, Wilson KS. Structure 6 363-376 (1998)
  7. Two "unrelated" families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites. Denessiouk KA, Lehtonen JV, Korpela T, Johnson MS. Protein Sci 7 1136-1146 (1998)
  8. Enzyme-mononucleotide interactions: three different folds share common structural elements for ATP recognition. Denessiouk KA, Lehtonen JV, Johnson MS. Protein Sci 7 1768-1771 (1998)
  9. Analysis of Soluble protein complexes in Shigella flexneri reveals the influence of temperature on the amount of lipopolysaccharide. Niu C, Shang N, Liao X, Feng E, Liu X, Wang D, Wang J, Huang P, Hua Y, Zhu L, Wang H. Mol Cell Proteomics 12 1250-1258 (2013)
  10. Catalytic loop motion in human glutathione synthetase: A molecular modeling approach. Dinescu A, Anderson ME, Cundari TR. Biochem Biophys Res Commun 353 450-456 (2007)
  11. A single mutation disrupts the pH-dependent dimerization of glycinamide ribonucleotide transformylase. Mullen CA, Jennings PA. J Mol Biol 276 819-827 (1998)
  12. Characterization of a cold-adapted glutathione synthetase from the psychrophile Pseudoalteromonas haloplanktis. Albino A, Marco S, Di Maro A, Chambery A, Masullo M, De Vendittis E. Mol Biosyst 8 2405-2414 (2012)
  13. Improving protein crystal quality by the without-oil microbatch method: crystallization and preliminary X-ray diffraction analysis of glutathione synthetase from Pseudoalteromonas haloplanktis. Merlino A, Russo Krauss I, Albino A, Pica A, Vergara A, Masullo M, De Vendittis E, Sica F. Int J Mol Sci 12 6312-6319 (2011)
  14. The testis-specific apoptosis related gene TTL.6 underwent adaptive evolution in the lineage leading to humans. Chen XH, Shi H, Liu XL, Su B. Gene 370 58-63 (2006)


Related citations provided by authors (7)

  1. Flexible Loop that is Novel Catalytic Machinery in a Ligase. Atomic Structure and Function of the Loopless Glutathione Synthetase. Kato H, Tanaka T, Yamaguchi H, Hara T, Nishioka T, Katsube Y, Oda J Biochemistry 33 4995- (1994)
  2. Mechanism-Based Inactivation of Glutathione Synthetase by Phosphinic Acid Transition-State Analogue. Hiratake J, Kato H, Oda J J. Am. Chem. Soc. 116 12059- (1994)
  3. Use of Adenosine (5')Polyphospho(5')Pyridoxals to Study the Substrate-Binding Region of Glutathione Synthetase from Escherichia Coli B. Hibi T, Kato H, Nishioka T, Oda J, Yamaguchi H, Katsube Y, Tanizawa K, Fukui T Biochemistry 32 1548- (1993)
  4. Flexibility Impaired by Mutations Revealed the Multifunctional Roles of the Loop in Glutathione Synthetase. Tanaka T, Yamaguchi H, Kato H, Nishioka T, Katsube Y, Oda J Biochemistry 32 12398- (1993)
  5. Three-Dimensional Structure of the Glutathione Synthetase from Escherichia Coli B at 2.0 A Resolution. Yamaguchi H, Kato H, Hata Y, Nishioka T, Kimura A, Oda J, Katsube Y J. Mol. Biol. 229 1083- (1993)
  6. Structural Studies on Glutathione Synthetase from Escherichia Coli B. Yamaguchi H, Kato H, Hata Y, Nishioka T, Oda J, Katsube Y Photon Factory Activity Report 9 85- (1992)
  7. Crystallization and Preliminary X-Ray Studies of Glutathione Synthetase from Escherichia Coli B. Kato H, Yamaguchi H, Hata Y, Nishioka T, Katsube Y, Oda J J. Mol. Biol. 209 503- (1989)

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