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protein metals Protein-protein interface(s) links
Lyase PDB id
2zcf
Jmol
Contents
Protein chains
198 a.a. *
212 a.a. *
Metals
_FE
_MG
Waters ×655
* Residue conservation analysis
PDB id:
2zcf
Name: Lyase
Title: Mutational study on alpha-gln90 of fe-type nitrile hydratase from rhodococcus sp. N771
Structure: Nitrile hydratase subunit alpha. Chain: a. Synonym: nitrilase, nhase. Engineered: yes. Mutation: yes. Nitrile hydratase subunit beta. Chain: b. Synonym: nitrilase, nhase. Engineered: yes
Source: Rhodococcus erythropolis. Organism_taxid: 1833. Gene: ntha. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: nthb.
Resolution:
1.43Å     R-factor:   0.170     R-free:   0.211
Authors: H.Takarada,Y.Kawano,K.Hashimoto,H.Nakayama,S.Ueda,M.Yohda, N.Kamiya,N.Dohmae,M.Maeda,M.Odaka,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref: H.Takarada et al. (2006). Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771. Biosci Biotechnol Biochem, 70, 881-889. PubMed id: 16636455 DOI: 10.1271/bbb.70.881
Date:
08-Nov-07     Release date:   20-Nov-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P13448  (NHAA_RHOER) -  Nitrile hydratase subunit alpha
Seq:
Struc: 		207 a.a.
198 a.a.*
Protein chain
Pfam   ArchSchema ?
P13449  (NHAB_RHOER) -  Nitrile hydratase subunit beta
Seq:
Struc: 		212 a.a.
212 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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: 10.1271/bbb.70.881 Biosci Biotechnol Biochem 70:881-889 (2006)
PubMed id: 16636455  
 
 
Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771.
H.Takarada, Y.Kawano, K.Hashimoto, H.Nakayama, S.Ueda, M.Yohda, N.Kamiya, N.Dohmae, M.Maeda, M.Odaka.
 
  ABSTRACT  
 
Nitrile hydratase (NHase) from Rhodococcus sp. N771 is a non-heme iron enzyme having post-translationally modified cysteine ligands, alphaCys112-SO2H and alphaCys114-SOH. We replaced alphaGln90, which is conserved in all known NHases and involved in the hydrogen-bond network around the catalytic center, with glutamic acid or asparagine. The kcat of alphaQ90E and alphaQ90N mutants decreased to 24% and 5% that of wild type respectively, but the effect of mutations on Km was not very significant. In both mutants, the alphaCys114-SOH modification appeared to be responsible for the catalysis as in native NHase. We crystallized the nitrosylated alphaQ90N mutant and determined its structure at a resolution of 1.43 A. The structure was basically identical to that of native nitrosylated NHase except for the mutated site and its vicinity. The structural difference between native and alphaQ90N mutant NHases suggested the importance of the hydrogen bond networks between alphaGln90 and the iron center for the catalytic activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
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.  
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.