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Lyase PDB id
2qdy
Jmol
Contents
Protein chains
197 a.a. *
211 a.a. *
Ligands
GOL ×6
IBN
Metals
_FE
_CL ×4
_MG ×3
Waters ×588
* Residue conservation analysis
PDB id:
2qdy
Name: Lyase
Title: Crystal structure of fe-type nhase from rhodococcus erythrop
Structure: Nitrile hydratase subunit alpha. Chain: a. Synonym: nitrilase, nhase. Nitrile hydratase subunit beta. Chain: b. Synonym: nitrilase, nhase. Ec: 4.2.1.84
Source: Rhodococcus erythropolis. Strain: aj270. Strain: aj270
Resolution:
1.30Å     R-factor:   0.131     R-free:   0.157
Authors: L.Song,J.Shi,Z.Xue,M.-X.Wang,S.Qian
Key ref: L.Song et al. (2007). High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism. Biochem Biophys Res Commun, 362, 319-324. PubMed id: 17716629 DOI: 10.1016/j.bbrc.2007.07.184
Date:
22-Jun-07     Release date:   13-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13448  (NHAA_RHOER) -  Nitrile hydratase subunit alpha
Seq:
Struc: 		207 a.a.
197 a.a.*
Protein chain
Pfam   ArchSchema ?
P13449  (NHAB_RHOER) -  Nitrile hydratase subunit beta
Seq:
Struc: 		212 a.a.
211 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.4.2.1.84  - Nitrile hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An aliphatic amide = a nitrile + H2O
aliphatic amide
 = nitrile
 + H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plastid   1 term 
  Biological process     nitrogen compound metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/j.bbrc.2007.07.184 Biochem Biophys Res Commun 362:319-324 (2007)
PubMed id: 17716629  
 
 
High resolution X-ray molecular structure of the nitrile hydratase from Rhodococcus erythropolis AJ270 reveals posttranslational oxidation of two cysteines into sulfinic acids and a novel biocatalytic nitrile hydration mechanism.
L.Song, M.Wang, J.Shi, Z.Xue, M.X.Wang, S.Qian.
 
  ABSTRACT  
 
The crystal structure of Fe-type nitrile hydratase from Rhodococcus erythropolis AJ270 was determined at 1.3A resolution. The two cysteine residues (alphaCys(112) and alphaCys(114)) equatorially coordinated to the ferric ion were post-translationally modified to cysteine sulfinic acids. A glutamine residue (alphaGln(90)) in the active center gave double conformations. Based on the interactions among the enzyme, substrate and water molecules, a new mechanism of biocatalysis of nitrile hydratase was proposed, in which the water molecule activated by the glutamine residue performed as the nucleophile to attack on the nitrile which was simultaneously interacted by another water molecule coordinated to the ferric ion.
 

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.  
20721414 D.H.Leng, D.X.Wang, Z.T.Huang, and M.X.Wang (2010).
Highly efficient and enantioselective biotransformations of β-lactam carbonitriles and carboxamides and their synthetic applications.
  Org Biomol Chem, 8, 4736-4743.  
19533706 W.Hu, Q.Luo, X.Ma, K.Wu, J.Liu, Y.Chen, S.Xiong, J.Wang, P.J.Sadler, and F.Wang (2009).
Arene control over thiolate to sulfinate oxidation in albumin by organometallic ruthenium anticancer complexes.
  Chemistry, 15, 6586-6594.  
18234830 K.Kubiak, and W.Nowak (2008).
Molecular dynamics simulations of the photoactive protein nitrile hydratase.
  Biophys J, 94, 3824-3838.  
18989922 P.Lugo-Mas, W.Taylor, D.Schweitzer, R.M.Theisen, L.Xu, J.Shearer, R.D.Swartz, M.C.Gleaves, A.Dipasquale, W.Kaminsky, and J.A.Kovacs (2008).
Properties of square-pyramidal alkyl-thiolate Fe(III) complexes, including an analogue of the unmodified form of nitrile hydratase.
  Inorg Chem, 47, 11228-11236.  
18721750 R.M.McCarty, and V.Bandarian (2008).
Deciphering deazapurine biosynthesis: pathway for pyrrolopyrimidine nucleosides toyocamycin and sangivamycin.
  Chem Biol, 15, 790-798.  
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.