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Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft.

Wang WC, Hsu WH, Chien FT, Chen CY
J Mol Biol 306 251-61 (2001)
Cited: 35 times
EuropePMC logo PMID: 11237598

Abstract

The N-carbamoyl-D-amino-acid amidohydrolase (D-NCAase) is used on an industrial scale for the production of D-amino acids. The crystal structure of D-NCAase was solved by multiple isomorphous replacement with anomalous scattering using xenon and gold derivatives, and refined to 1.95 A resolution, to an R-factor of 18.6 %. The crystal structure shows a four-layer alpha/beta fold with two six-stranded beta sheets packed on either side by two alpha helices. One exterior layer faces the solvent, whereas the other one is buried and involved in the tight intersubunit contacts. A long C-terminal fragment extends from a monomer to a site near a dyad axis, and associates with another monomer to form a small and hydrophobic cavity, where a xenon atom can bind. Site-directed mutagenesis of His129, His144 and His215 revealed strict geometric requirements of these conserved residues to maintain a stable conformation of a putative catalytic cleft. A region located within this cleft involving Cys172, Glu47, and Lys127 is proposed for D-NCAase catalysis and is similar to the Cys-Asp-Lys site of N-carbamoylsarcosine amidohydrolase. The homologous active-site framework of these enzymes with distinct structures suggests convergent evolution of a common catalytic mechanism.

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  4. Identification of essential residues in apolipoprotein N-acyl transferase, a member of the CN hydrolase family. Vidal-Ingigliardi D, Lewenza S, Buddelmeijer N. J Bacteriol 189 4456-4464 (2007)
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  6. Improvement of oxidative and thermostability of N-carbamyl-d-amino Acid amidohydrolase by directed evolution. Oh KH, Nam SH, Kim HS. Protein Eng 15 689-695 (2002)
  7. The essential Escherichia coli apolipoprotein N-acyltransferase (Lnt) exists as an extracytoplasmic thioester acyl-enzyme intermediate. Buddelmeijer N, Young R. Biochemistry 49 341-346 (2010)
  8. Crystal structure of a putative CN hydrolase from yeast. Kumaran D, Eswaramoorthy S, Gerchman SE, Kycia H, Studier FW, Swaminathan S. Proteins 52 283-291 (2003)
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  11. Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution. Sakai N, Tajika Y, Yao M, Watanabe N, Tanaka I. Proteins 57 869-873 (2004)
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  13. Glutamine amidotransferase activity of NAD+ synthetase from Mycobacterium tuberculosis depends on an amino-terminal nitrilase domain. Bellinzoni M, Buroni S, Pasca MR, Guglierame P, Arcesi F, De Rossi E, Riccardi G. Res Microbiol 156 173-177 (2005)
  14. Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. Sekula B, Ruszkowski M, Malinska M, Dauter Z. Front Plant Sci 7 350 (2016)
  15. HylA, an alternative hydrolase for initiation of catabolism of the phenylurea herbicide linuron in Variovorax sp. strains. Bers K, Batisson I, Proost P, Wattiez R, De Mot R, Springael D. Appl Environ Microbiol 79 5258-5263 (2013)
  16. The cyanide hydratase from Neurospora crassa forms a helix which has a dimeric repeat. Dent KC, Weber BW, Benedik MJ, Sewell BT. Appl Microbiol Biotechnol 82 271-278 (2009)
  17. Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans. Wang WC, Chiu WC, Hsu SK, Wu CL, Chen CY, Liu JS, Hsu WH. J Mol Biol 342 155-169 (2004)
  18. Enhancing oxidative resistance of Agrobacterium radiobacter N-carbamoyl D-amino acid amidohydrolase by engineering solvent-accessible methionine residues. Roger Chien HC, Hsu CL, Hu HY, Wang WC, Hsu WH. Biochem Biophys Res Commun 297 282-287 (2002)
  19. Molecular simulations to determine the chelating mechanisms of various metal ions to the His-tag motif: a preliminary study. Liu HL, Ho Y, Hsu CM. J Biomol Struct Dyn 21 31-41 (2003)
  20. The crystal structure of XC1258 from Xanthomonas campestris: a putative procaryotic Nit protein with an arsenic adduct in the active site. Chin KH, Tsai YD, Chan NL, Huang KF, Wang AH, Chou SH. Proteins 69 665-671 (2007)
  21. Improving the thermostability of N-carbamyl-D-amino acid amidohydrolase by error-prone PCR. Yu H, Li J, Zhang D, Yang Y, Jiang W, Yang S. Appl Microbiol Biotechnol 82 279-285 (2009)
  22. Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism. Maurer D, Lohkamp B, Krumpel M, Widersten M, Dobritzsch D. Biochem J 475 2395-2416 (2018)
  23. Probing an Interfacial Surface in the Cyanide Dihydratase from Bacillus pumilus, A Spiral Forming Nitrilase. Park JM, Mulelu A, Sewell BT, Benedik MJ. Front Microbiol 6 1479 (2015)
  24. Decoding the Rich Biological Properties of Noble Gases: How Well Can We Predict Noble Gas Binding to Diverse Proteins? Winkler DA, Katz I, Farjot G, Warden AC, Thornton AW. ChemMedChem 13 1931-1938 (2018)
  25. Burkholderia genome analysis reveals new enzymes belonging to the nitrilase superfamily. The amidase of Burkholderia cepacia (hospital isolate). Novo C, Tata R, Clemente A, Brown PR. Int J Biol Macromol 33 175-182 (2003)
  26. Novel amidases of two Aminobacter sp. strains: Biotransformation experiments and elucidation of gene sequences. Engel U, Syldatk C, Rudat J. AMB Express 2 33 (2012)
  27. Regulation of hydantoin-hydrolyzing enzyme expression in Agrobacterium tumefaciens strain RU-AE01. Jiwaji M, Dorrington RA. Appl Microbiol Biotechnol 84 1169-1179 (2009)


Related citations provided by authors (1)

  1. Expression, crystallization and preliminary X-ray diffraction studies of N-carbamyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter. Hsu W-H, Chien F-T, Hsu CL, Wang TC, Yuan HS, Wang W-C Acta Crystallogr. D Biol. Crystallogr. 55 694-695 (1999)

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