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Characterization of a novel Ser-cisSer-Lys catalytic triad in comparison with the classical Ser-His-Asp triad.

Shin S, Yun YS, Koo HM, Kim YS, Choi KY, Oh BH
J Biol Chem 278 24937-43 (2003)
Related entries: 1o9n, 1o9o, 1o9q, 1obi, 1obj, 1obk, 1obl, 1och, 1ock, 1ocl, 1ocm

Cited: 28 times
EuropePMC logo PMID: 12711609

Abstract

Amidase signature family enzymes, which are widespread in nature, contain a newly identified Ser-cisSer-Lys catalytic triad in which the peptide bond between Ser131 and the preceding residue Gly130 is in a cis configuration. In order to characterize the property of the novel triad, we have determined the structures of five mutant malonamidase E2 enzymes that contain a Cys-cisSer-Lys, Ser-cisAla-Lys, or Ser-cisSer-Ala triad or a substitution of Gly130 with alanine. Cysteine cannot replace the role of Ser155 due to a hyper-reactivity of the residue, which results in the modification of the cysteine to cysteinyl sulfinic acid, most likely inside the expression host cells. The lysine residue plays a structural as well as a catalytic role, since the substitution of the residue with alanine disrupts the active site structure completely. The two observations are in sharp contrast with the consequences of the corresponding substitutions in the classical Ser-His-Asp triad. Structural data on the mutant containing the Ser-cisAla-Lys triad convincingly suggest that Ser131 plays an analogous catalytic role as the histidine of the Ser-His-Asp triad. The unusual cis configuration of Ser131 appears essential for the precise contacts of this residue with the other triad residues, as indicated by the near invariance of the preceding glycine residue (Gly130), structural data on the G130A mutant, and by a modeling experiment. The data provide a deep understanding of the role of each residue of the new triad at the atomic level and demonstrate that the new triad is a catalytic device distinctively different from the classical triad or its variants.

Reviews citing this publication (5)

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Articles citing this publication (23)

  1. A novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by Variovorax sp. strain SRS16. Bers K, Leroy B, Breugelmans P, Albers P, Lavigne R, Sørensen SR, Aamand J, De Mot R, Wattiez R, Springael D. Appl Environ Microbiol 77 8754-8764 (2011)
  2. Purification and characterization of allophanate hydrolase (AtzF) from Pseudomonas sp. strain ADP. Shapir N, Sadowsky MJ, Wackett LP. J Bacteriol 187 3731-3738 (2005)
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  5. Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme. Wu J, Bu W, Sheppard K, Kitabatake M, Kwon ST, Söll D, Smith JL. J Mol Biol 391 703-716 (2009)
  6. QM/MM modelling of oleamide hydrolysis in fatty acid amide hydrolase (FAAH) reveals a new mechanism of nucleophile activation. Lodola A, Mor M, Hermann JC, Tarzia G, Piomelli D, Mulholland AJ. Chem Commun (Camb) 4399-4401 (2005)
  7. Pharmacological convergence reveals a lipid pathway that regulates C. elegans lifespan. Chen AL, Lum KM, Lara-Gonzalez P, Ogasawara D, Cognetta AB, To A, Parsons WH, Simon GM, Desai A, Petrascheck M, Bar-Peled L, Cravatt BF. Nat Chem Biol 15 453-462 (2019)
  8. Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells. Nolan LM, Cain AK, Clamens T, Furniss RCD, Manoli E, Sainz-Polo MA, Dougan G, Albesa-Jové D, Parkhill J, Mavridou DAI, Filloux A. Nat Microbiol 6 1199-1210 (2021)
  9. X-ray structure of the amidase domain of AtzF, the allophanate hydrolase from the cyanuric acid-mineralizing multienzyme complex. Balotra S, Newman J, Cowieson NP, French NG, Campbell PM, Briggs LJ, Warden AC, Easton CJ, Peat TS, Scott C. Appl Environ Microbiol 81 470-480 (2015)
  10. Structure and function of allophanate hydrolase. Fan C, Li Z, Yin H, Xiang S. J Biol Chem 288 21422-21432 (2013)
  11. The structure of allophanate hydrolase from Granulibacter bethesdensis provides insights into substrate specificity in the amidase signature family. Lin Y, St Maurice M. Biochemistry 52 690-700 (2013)
  12. Identification of a thermostable and enantioselective amidase from the thermoacidophilic archaeon Sulfolobus tokodaii strain 7. Suzuki Y, Ohta H. Protein Expr Purif 45 368-373 (2006)
  13. The mechanism of the Ser-(cis)Ser-Lys catalytic triad of peptide amidases. Cerqueira NMFSA, Moorthy H, Fernandes PA, Ramos MJ. Phys Chem Chem Phys 19 12343-12354 (2017)
  14. Salt-tolerant and thermostable glutaminases of cryptococcus species form a new glutaminase family. Ito K, Umitsuki G, Oguma T, Koyama Y. Biosci Biotechnol Biochem 75 1317-1324 (2011)
  15. Understanding structural/functional properties of amidase from Rhodococcus erythropolis by computational approaches. Han WW, Wang Y, Zhou YH, Yao Y, Li ZS, Feng Y. J Mol Model 15 481-487 (2009)
  16. Characterization of bacterial NMN deamidase as a Ser/Lys hydrolase expands diversity of serine amidohydrolases. Sorci L, Brunetti L, Cialabrini L, Mazzola F, Kazanov MD, D'Auria S, Ruggieri S, Raffaelli N. FEBS Lett 588 1016-1023 (2014)
  17. Crystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2 - insight into the structural factors for substrate specificity. Arima J, Shimone K, Miyatani K, Tsunehara Y, Isoda Y, Hino T, Nagano S. FEBS J 283 337-349 (2016)
  18. Oligomerization of Sulfolobus solfataricus signature amidase is promoted by acidic pH and high temperature. Scotto D'Abusco A, Casadio R, Tasco G, Giangiacomo L, Giartosio A, Calamia V, Di Marco S, Chiaraluce R, Consalvi V, Scandurra R, Politi L. Archaea 1 411-423 (2005)
  19. Arg-158 is critical in both binding the substrate and stabilizing the transition-state oxyanion for the enzymatic reaction of malonamidase E2. Yun YS, Lee W, Shin S, Oh BH, Choi KY. J Biol Chem 281 40057-40064 (2006)
  20. In Silico and In Vitro Analysis of Major Cannabis-Derived Compounds as Fatty Acid Amide Hydrolase Inhibitors. Criscuolo E, De Sciscio ML, Fezza F, Maccarrone M. Molecules 26 E48 (2020)
  21. Structure-Based Engineering of Amidase from Pantoea sp. for Efficient 2-Chloronicotinic Acid Biosynthesis. Tang XL, Jin JQ, Wu ZM, Jin LQ, Zheng RC, Zheng YG. Appl Environ Microbiol 85 e02471-18 (2019)
  22. Using directed evolution to probe the substrate specificity of mandelamide hydrolase. Wang PF, Yep A, Kenyon GL, McLeish MJ. Protein Eng Des Sel 22 103-110 (2009)
  23. The Structure and Function of Biomaterial Endolysin EFm1 from E. faecalis Phage. Zhou X, Zeng X, Wang L, Zheng Y, Zhang G, Cheng W. Materials (Basel) 15 4879 (2022)


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