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PDBsum entry 1nba

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protein ligands Protein-protein interface(s) links
Hydrolase(in linear amides) PDB id
1nba
Jmol
Contents
Protein chains
253 a.a. *
Ligands
SO4 ×4
Waters ×431
* Residue conservation analysis
PDB id:
1nba
Name: Hydrolase(in linear amides)
Title: Crystal structure analysis, refinement and enzymatic reaction mechanism of n-carbamoylsarcosine amidohydrolase from arthrobacter sp. At 2.0 angstroms resolution
Structure: N-carbamoylsarcosine amidohydrolase. Chain: a, b, c, d. Engineered: yes
Source: Arthrobacter sp.. Organism_taxid: 1667
Biol. unit: Tetramer (from PQS)
Resolution:
2.00Å     R-factor:   0.186    
Authors: M.J.Romao,D.Turk,F.-Z.Gomis-Ruth,R.Huber,G.Schumacher, H.Mollering,L.Russmann
Key ref:
M.J.Romão et al. (1992). Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 A resolution. J Mol Biol, 226, 1111-1130. PubMed id: 1381445 DOI: 10.1016/0022-2836(92)91056-U
Date:
18-May-92     Release date:   22-Jun-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P32400  (CSH_ARTSP) -  N-carbamoylsarcosine amidase
Seq:
Struc:
264 a.a.
253 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.59  - N-carbamoylsarcosine amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Creatine Biosynthesis
      Reaction: N-carbamoylsarcosine + H2O = sarcosine + CO2 + NH3
N-carbamoylsarcosine
+ H(2)O
= sarcosine
+ CO(2)
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0022-2836(92)91056-U J Mol Biol 226:1111-1130 (1992)
PubMed id: 1381445  
 
 
Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2.0 A resolution.
M.J.Romão, D.Turk, F.X.Gomis-Rüth, R.Huber, G.Schumacher, H.Möllering, L.Rüssmann.
 
  ABSTRACT  
 
N-carbamoylsarcosine amidohydrolase from Arthrobacter sp., a tetramer of polypeptides with 264 amino acid residues each, has been crystallized and its structure solved and refined at 2.0 A resolution, to a crystallographic R-factor of 18.6%. The crystals employed in the analysis contain one tetramer of 116,000 M(r) in the asymmetric unit. The structure determination proceeded by multiple isomorphous replacement, followed by solvent-flattening and density averaging about the local diads within the tetramer. In the final refined model, the root-mean-square deviation from ideality is 0.01 A for bond distances and 2.7 degrees for bond angles. The asymmetric unit consists of 7853 protein atoms, 431 water molecules and four sulfate ions bound into the putative active site clefts in each subunit. One subunit contains a central six-stranded parallel beta-pleated sheet packed by helices on both sides. On one side, two helices face the solvent, while two of the helices on the other side are buried in the tight intersubunit contacts. The catalytic center of the enzyme, tentatively identified by inhibitor binding, is located at the interface between two subunits and involves residues from both. It is suggested that the nucleophilic group involved in hydrolysis of the substrate is the thiol group of Cys117 and a nucleophilic addition-elimination mechanism is proposed.
 
  Selected figure(s)  
 
Figure 0.
Fig. 0.
Figure 9.
Figure 9. Stereo-ribbon diagram (Priestle, 1988) of 1 subunit fo CSHase. The labels follow Table 12. The bound sulfate on s abeled.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 226, 1111-1130) copyright 1992.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19932181 H.B.Luo, H.Zheng, M.D.Zimmerman, M.Chruszcz, T.Skarina, O.Egorova, A.Savchenko, A.M.Edwards, and W.Minor (2010).
Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.
  J Struct Biol, 169, 304-311.
PDB code: 3eef
17382284 G.Hu, A.B.Taylor, L.McAlister-Henn, and P.J.Hart (2007).
Crystal structure of the yeast nicotinamidase Pnc1p.
  Arch Biochem Biophys, 461, 66-75.
PDB code: 2h0r
16199669 J.Caruthers, F.Zucker, E.Worthey, P.J.Myler, F.Buckner, W.Van Voorhuis, C.Mehlin, E.Boni, T.Feist, J.Luft, S.Gulde, A.Lauricella, O.Kaluzhniy, L.Anderson, I.Le Trong, M.A.Holmes, T.Earnest, M.Soltis, K.O.Hodgson, W.G.Hol, and E.A.Merritt (2005).
Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily.
  Protein Sci, 14, 2887-2894.
PDB codes: 1x9g 1xn4 1yzv
15200410 N.Horiba, S.Masuda, A.Takeuchi, H.Saito, M.Okuda, and K.Inui (2004).
Gene expression variance based on random sequencing in rat remnant kidney.
  Kidney Int, 66, 29-45.  
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.  
11371533 R.W.Eaton (2001).
Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B.
  J Bacteriol, 183, 3689-3703.  
11106482 S.J.Cooper, C.D.Garner, W.R.Hagen, P.F.Lindley, and S.Bailey (2000).
Hybrid-cluster protein (HCP) from Desulfovibrio vulgaris (Hildenborough) at 1.6 A resolution.
  Biochemistry, 39, 15044-15054.
PDB codes: 1e1d 1e2u
10903946 T.Nakai, T.Hasegawa, E.Yamashita, M.Yamamoto, T.Kumasaka, T.Ueki, H.Nanba, Y.Ikenaka, S.Takahashi, M.Sato, and T.Tsukihara (2000).
Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases.
  Structure, 8, 729-737.
PDB code: 1erz
  10390238 N.Lemaitre, W.Sougakoff, C.Truffot-Pernot, and V.Jarlier (1999).
Characterization of new mutations in pyrazinamide-resistant strains of Mycobacterium tuberculosis and identification of conserved regions important for the catalytic activity of the pyrazinamidase PncA.
  Antimicrob Agents Chemother, 43, 1761-1763.  
9782055 C.Colovos, D.Cascio, and T.O.Yeates (1998).
The 1.8 A crystal structure of the ycaC gene product from Escherichia coli reveals an octameric hydrolase of unknown specificity.
  Structure, 6, 1329-1337.
PDB code: 1yac
9218780 A.Humm, E.Fritsche, S.Steinbacher, and R.Huber (1997).
Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis.
  EMBO J, 16, 3373-3385.
PDB codes: 1jdw 2jdw 3jdw 4jdw
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
  9165062 W.Baumeister, Z.Cejka, M.Kania, and E.Seemüller (1997).
The proteasome: a macromolecular assembly designed to confine proteolysis to a nanocompartment.
  Biol Chem, 378, 121-130.  
  8726014 R.Frothingham, W.A.Meeker-O'Connell, E.A.Talbot, J.W.George, and K.N.Kreuzer (1996).
Identification, cloning, and expression of the Escherichia coli pyrazinamidase and nicotinamidase gene, pncA.
  Antimicrob Agents Chemother, 40, 1426-1431.  
8702766 T.Hisano, Y.Hata, T.Fujii, J.Q.Liu, T.Kurihara, N.Esaki, and K.Soda (1996).
Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.
  J Biol Chem, 271, 20322-20330.
PDB code: 1jud
8143752 J.Caldeira, P.N.Palma, M.Regalla, J.Lampreia, J.Calvete, W.Schäfer, J.Legall, I.Moura, and J.J.Moura (1994).
Primary sequence, oxidation-reduction potentials and tertiary-structure prediction of Desulfovibrio desulfuricans ATCC 27774 flavodoxin.
  Eur J Biochem, 220, 987-995.  
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.