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PDBsum entry 1fo6

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
1fo6
Jmol
Contents
Protein chains
302 a.a. *
Metals
_XE ×2
Waters ×722
* Residue conservation analysis
PDB id:
1fo6
Name: Hydrolase
Title: Crystal structure analysis of n-carbamoyl-d-amino-acid amidohydrolase
Structure: N-carbamoyl-d-amino-acid amidohydrolase. Chain: a, b, c, d. Engineered: yes
Source: Agrobacterium tumefaciens. Organism_taxid: 358. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.95Å     R-factor:   0.187     R-free:   0.239
Authors: W.-C.Wang,W.-H.Hsu,F.-T.Chien,C.-Y.Chen
Key ref:
W.C.Wang et al. (2001). 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. J Mol Biol, 306, 251-261. PubMed id: 11237598 DOI: 10.1006/jmbi.2000.4380
Date:
25-Aug-00     Release date:   29-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q44185  (DCAS_RHIRD) -  N-carbamoyl-D-amino acid hydrolase
Seq:
Struc:
304 a.a.
302 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.77  - N-carbamoyl-D-amino-acid hydrolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N-carbamoyl-D-amino acid + H2O = D-amino acid + NH3 + CO2
N-carbamoyl-D-amino acid
+ H(2)O
= D-amino acid
+ NH(3)
+ CO(2)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nitrogen compound metabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.4380 J Mol Biol 306:251-261 (2001)
PubMed id: 11237598  
 
 
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.
W.C.Wang, W.H.Hsu, F.T.Chien, C.Y.Chen.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Chemical reaction catalyzed by D-NCAase.
Figure 5.
Figure 5. (a) Structural analysis of three catalytically important residues His129, His144, and His215 as identified by mutagenesis. The two subunits A and B are colored in green and red, respectively. The histidine residues, His129, His144 and His215 are in purple, whereas Cys172 is in red. (b) A hydrogen-bonding network among HisA129, AspA174, IleA171, and TyrB298. (c) A hydrogen-bonding network among His144, His133, Glu146 and Wat84.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 306, 251-261) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19830420 S.Martínez-Rodríguez, A.I.Martínez-Gómez, F.Rodríguez-Vico, J.M.Clemente-Jiménez, and F.J.Las Heras-Vázquez (2010).
Carbamoylases: characteristics and applications in biotechnological processes.
  Appl Microbiol Biotechnol, 85, 441-458.  
18985337 H.Yu, J.Li, D.Zhang, Y.Yang, W.Jiang, and S.Yang (2009).
Improving the thermostability of N-carbamyl-D-amino acid amidohydrolase by error-prone PCR.
  Appl Microbiol Biotechnol, 82, 279-285.  
18946669 K.C.Dent, B.W.Weber, M.J.Benedik, and B.T.Sewell (2009).
The cyanide hydratase from Neurospora crassa forms a helix which has a dimeric repeat.
  Appl Microbiol Biotechnol, 82, 271-278.  
19053248 K.T.Barglow, K.S.Saikatendu, M.H.Bracey, R.Huey, G.M.Morris, A.J.Olson, R.C.Stevens, and B.F.Cravatt (2008).
Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes.
  Biochemistry, 47, 13514-13523.
PDB code: 2w1v
17565494 C.Etchebest, C.Benros, A.Bornot, A.C.Camproux, and A.G.de Brevern (2007).
A reduced amino acid alphabet for understanding and designing protein adaptation to mutation.
  Eur Biophys J, 36, 1059-1069.  
17307742 C.L.Hung, J.H.Liu, W.C.Chiu, S.W.Huang, J.K.Hwang, and W.C.Wang (2007).
Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad.
  J Biol Chem, 282, 12220-12229.
PDB codes: 2dyu 2dyv 2e2k 2e2l
17416655 D.Vidal-Ingigliardi, S.Lewenza, and N.Buddelmeijer (2007).
Identification of essential residues in apolipoprotein N-acyl transferase, a member of the CN hydrolase family.
  J Bacteriol, 189, 4456-4464.  
17442671 J.Andrade, A.Karmali, M.A.Carrondo, and C.Frazão (2007).
Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state.
  J Biol Chem, 282, 19598-19605.
PDB code: 2uxy
17640068 K.H.Chin, Y.D.Tsai, N.L.Chan, K.F.Huang, A.H.Wang, and S.H.Chou (2007).
The crystal structure of XC1258 from Xanthomonas campestris: a putative procaryotic Nit protein with an arsenic adduct in the active site.
  Proteins, 69, 665-671.
PDB code: 2e11
  17012795 Y.D.Tsai, K.H.Chin, H.L.Shr, F.P.Gao, P.C.Lyu, A.H.Wang, and S.H.Chou (2006).
Cloning, crystallization and preliminary X-ray study of XC1258, a CN-hydrolase superfamily protein from Xanthomonas campestris.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 999.  
16083508 M.Podar, J.R.Eads, and T.H.Richardson (2005).
Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study.
  BMC Evol Biol, 5, 42.  
15390259 N.Sakai, Y.Tajika, M.Yao, N.Watanabe, and I.Tanaka (2004).
Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution.
  Proteins, 57, 869-873.
PDB code: 1j31
12709423 C.Y.Chen, W.C.Chiu, J.S.Liu, W.H.Hsu, and W.C.Wang (2003).
Structural basis for catalysis and substrate specificity of Agrobacterium radiobacter N-carbamoyl-D-amino acid amidohydrolase.
  J Biol Chem, 278, 26194-26201.  
12832781 D.Dobritzsch, Z.Gojković, B.Andersen, and J.Piskur (2003).
Crystallization and preliminary X-ray analysis of beta-alanine synthase from the yeast Saccharomyces kluyveri.
  Acta Crystallogr D Biol Crystallogr, 59, 1267-1269.  
12833551 D.Kumaran, S.Eswaramoorthy, S.E.Gerchman, H.Kycia, F.W.Studier, and S.Swaminathan (2003).
Crystal structure of a putative CN hydrolase from yeast.
  Proteins, 52, 283-291.
PDB code: 1f89
14573947 M.L.Quillin, and B.W.Matthews (2003).
Selling candles in a post-Edison world: phasing with noble gases bound within engineered sites.
  Acta Crystallogr D Biol Crystallogr, 59, 1930-1934.  
14534321 S.Lundgren, Z.Gojković, J.Piskur, and D.Dobritzsch (2003).
Yeast beta-alanine synthase shares a structural scaffold and origin with dizinc-dependent exopeptidases.
  J Biol Chem, 278, 51851-51862.
PDB codes: 1r3n 1r43
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.