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PDBsum entry 1v29
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protein metals Protein-protein interface(s) links
Lyase PDB id
1v29

 

 

 

 

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Contents
Protein chains
203 a.a. *
229 a.a. *
Metals
_CO
Waters ×119
* Residue conservation analysis
PDB id:
1v29
Name: Lyase
Title: Crystal structure of nitrile hydratase from a thermophile bacillus smithii
Structure: Nitrile hydratase a chain. Chain: a. Nitrile hydratase b chain. Chain: b. Ec: 4.2.1.84
Source: Bacillus smithii. Organism_taxid: 1479. Organism_taxid: 1479
Biol. unit: 60mer (from PDB file)
Resolution:
2.60Å     R-factor:   0.187     R-free:   0.226
Authors: S.Hourai,M.Miki,Y.Takashima,S.Mitsuda,K.Yanagi
Key ref: S.Hourai et al. (2003). Crystal structure of nitrile hydratase from a thermophilic Bacillus smithii. Biochem Biophys Res Commun, 312, 340-345. PubMed id: 14637142 DOI: 10.1016/j.bbrc.2003.10.124
Date:
09-Oct-03     Release date:   09-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q84FS5  (Q84FS5_9BACI) -  nitrile hydratase from Bacillus sp. RAPc8
Seq:
Struc: 		216 a.a.
203 a.a.*
Protein chain
No UniProt id for this chain
Struc: 229 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.4.2.1.84  - nitrile hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: an aliphatic primary amide = an aliphatic nitrile + H2O
aliphatic primary amide
 = aliphatic nitrile
 + H2O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1016/j.bbrc.2003.10.124 Biochem Biophys Res Commun 312:340-345 (2003)
PubMed id: 14637142  
 
 
Crystal structure of nitrile hydratase from a thermophilic Bacillus smithii.
S.Hourai, M.Miki, Y.Takashima, S.Mitsuda, K.Yanagi.
 
  ABSTRACT  
 
The crystal structure of the nitrile hydratase (NHase) from Bacillus smithii SC-J05-1 was determined. Our analysis of the structure shows that some residues that seem to be responsible for substrate recognition are different from those of other NHases. In particular, the Phe52 in the beta subunit of NHase from B. smithii covers the metal center partially like a small lid and narrows the active site cleft. It is well known that the NHase from B. smithii especially prefers aliphatic nitriles for its substrate rather than aromatic ones, and we can now infer that the Phe52 residue may play a key role in the substrate specificity for this enzyme. This finding leads us to suggest that substitution of these residues may alter the substrate specificity of the enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21380438 S.van Pelt, M.Zhang, L.G.Otten, J.Holt, D.Y.Sorokin, F.van Rantwijk, G.W.Black, J.J.Perry, and R.A.Sheldon (2011).
Probing the enantioselectivity of a diverse group of purified cobalt-centred nitrile hydratases.
  Org Biomol Chem, 9, 3011-3019.  
20500830 D.H.Haft, M.K.Basu, and D.A.Mitchell (2010).
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family.
  BMC Biol, 8, 70.  
20221653 Y.Yamanaka, K.Hashimoto, A.Ohtaki, K.Noguchi, M.Yohda, and M.Odaka (2010).
Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase.
  J Biol Inorg Chem, 15, 655-665.
PDB codes: 3a8g 3a8h 3a8l 3a8m 3a8o
19346246 Z.Zhou, Y.Hashimoto, and M.Kobayashi (2009).
Self-subunit Swapping Chaperone Needed for the Maturation of Multimeric Metalloenzyme Nitrile Hydratase by a Subunit Exchange Mechanism Also Carries Out the Oxidation of the Metal Ligand Cysteine Residues and Insertion of Cobalt.
  J Biol Chem, 284, 14930-14938.  
18948265 K.Hashimoto, H.Suzuki, K.Taniguchi, T.Noguchi, M.Yohda, and M.Odaka (2008).
Catalytic Mechanism of Nitrile Hydratase Proposed by Time-resolved X-ray Crystallography Using a Novel Substrate, tert-Butylisonitrile.
  J Biol Chem, 283, 36617-36623.
PDB codes: 2zpb 2zpe 2zpf 2zpg 2zph 2zpi
18234830 K.Kubiak, and W.Nowak (2008).
Molecular dynamics simulations of the photoactive protein nitrile hydratase.
  Biophys J, 94, 3824-3838.  
18804061 K.Taniguchi, K.Murata, Y.Murakami, S.Takahashi, T.Nakamura, K.Hashimoto, H.Koshino, N.Dohmae, M.Yohda, T.Hirose, M.Maeda, and M.Odaka (2008).
Novel catalytic activity of nitrile hydratase from Rhodococcus sp. N771.
  J Biosci Bioeng, 106, 174-179.  
18809911 Z.Zhou, Y.Hashimoto, K.Shiraki, and M.Kobayashi (2008).
Discovery of posttranslational maturation by self-subunit swapping.
  Proc Natl Acad Sci U S A, 105, 14849-14854.  
17333306 L.Peplowski, K.Kubiak, and W.Nowak (2007).
Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides.
  J Mol Model, 13, 725-730.  
17150969 S.Mitra, and R.C.Holz (2007).
Unraveling the catalytic mechanism of nitrile hydratases.
  J Biol Chem, 282, 7397-7404.  
16636455 H.Takarada, Y.Kawano, K.Hashimoto, H.Nakayama, S.Ueda, M.Yohda, N.Kamiya, N.Dohmae, M.Maeda, and M.Odaka (2006).
Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771.
  Biosci Biotechnol Biochem, 70, 881-889.
PDB code: 2zcf
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 codes are shown on the right.

 

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