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Lyase PDB id
2ahj
Jmol
Contents
Protein chains
194 a.a. *
211 a.a. *
Ligands
SO4 ×3
_NO ×2
DIO ×2
Metals
_FE ×2
_ZN ×2
Waters ×689
* Residue conservation analysis
PDB id:
2ahj
Name: Lyase
Title: Nitrile hydratase complexed with nitric oxide
Structure: Nitrile hydratase. Chain: a, c. Synonym: nhase. Other_details: in nitrosylated state (inactive form). Nitrile hydratase. Chain: b, d. Synonym: nhase. Other_details: in nitrosylated state (inactive form)
Source: Rhodococcus erythropolis. Organism_taxid: 1833. Strain: sp. N-771. Strain: sp. N-771
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.179     R-free:   0.228
Authors: S.Nagashima,M.Nakasako,N.Dohmae,M.Tsujimura,K.Takio,M.Odaka, M.Yohda,N.Kamiya,I.Endo
Key ref: S.Nagashima et al. (1998). Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms. Nat Struct Biol, 5, 347-351. PubMed id: 9586994 DOI: 10.1038/nsb0598-347
Date:
24-Dec-97     Release date:   27-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13448  (NHAA_RHOER) -  Nitrile hydratase subunit alpha
Seq:
Struc: 		207 a.a.
194 a.a.*
Protein chains
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, C, D: 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: 10.1038/nsb0598-347 Nat Struct Biol 5:347-351 (1998)
PubMed id: 9586994  
 
 
Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.
S.Nagashima, M.Nakasako, N.Dohmae, M.Tsujimura, K.Takio, M.Odaka, M.Yohda, N.Kamiya, I.Endo.
 
  ABSTRACT  
 
The iron-containing nitrile hydratase (NHase) is a photoreactive enzyme that is inactivated in the dark because of persistent association with NO and activated by photo-dissociation of NO. The crystal structure at 1.7 A resolution and mass spectrometry revealed the structure of the non-heme iron catalytic center in the nitrosylated state. Two Cys residues coordinated to the iron were post-translationally modified to Cys-sulfenic and -sulfinic acids. Together with another oxygen atom of the Ser ligand, these modifications induced a claw setting of oxygen atoms capturing an NO molecule. This unprecedented structure is likely to enable the photo-regulation of NHase and will provide an excellent model for designing photo-controllable chelate complexes and, ultimately, proteins.
 

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).
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PDB codes: 3a8g 3a8h 3a8l 3a8m 3a8o
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Iron and Cobalt Complexes of 2,6-Diacetylpyridine-bis(R-thiosemicarbazone) (R=H, phenyl) Showing Unprecedented Ligand Deviation from Planarity.
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Substrate binding preferences and pka determinations of a nitrile hydratase model complex: variable solvent coordination to [(bmmp-TASN)Fe]OTf.
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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.
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PDB codes: 2zpb 2zpe 2zpf 2zpg 2zph 2zpi
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Sulfur K-edge XAS and DFT studies on NiII complexes with oxidized thiolate ligands: implications for the roles of oxidized thiolates in the active sites of Fe and Co nitrile hydratase.
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17277050 A.Klink, B.Elsner, K.Strube, and R.Cramm (2007).
Characterization of the signaling domain of the NO-responsive regulator NorR from Ralstonia eutropha H16 by site-directed mutagenesis.
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17698201 B.W.Smucker, M.J.Vanstipdonk, and D.M.Eichhorn (2007).
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18019494 C.A.Joseph, and M.J.Maroney (2007).
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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.
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PDB code: 2e11
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.
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17330219 L.Song, M.Wang, X.Yang, and S.Qian (2007).
Purification and characterization of the enantioselective nitrile hydratase from Rhodococcus sp. AJ270.
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17150969 S.Mitra, and R.C.Holz (2007).
Unraveling the catalytic mechanism of nitrile hydratases.
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16357966 A.Christensen, C.Mayer, F.Jensen, A.D.Bond, and C.J.McKenzie (2006).
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16520978 C.Y.Chiang, and M.Y.Darensbourg (2006).
Iron nitrosyl complexes as models for biological nitric oxide transfer reagents.
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16807974 E.I.Solomon, S.I.Gorelsky, and A.Dey (2006).
Metal-thiolate bonds in bioinorganic chemistry.
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16418856 E.van der Linden, T.Burgdorf, A.L.de Lacey, T.Buhrke, M.Scholte, V.M.Fernandez, B.Friedrich, and S.P.Albracht (2006).
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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
16492780 J.G.McCoy, L.J.Bailey, E.Bitto, C.A.Bingman, D.J.Aceti, B.G.Fox, and G.N.Phillips (2006).
Structure and mechanism of mouse cysteine dioxygenase.
  Proc Natl Acad Sci U S A, 103, 3084-3089.
PDB code: 2atf
  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.
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15942729 A.Karlsson, J.V.Parales, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (2005).
NO binding to naphthalene dioxygenase.
  J Biol Inorg Chem, 10, 483-489.
PDB codes: 1uuv 1uuw
16136617 E.Bourles, R.Alves de Sousa, E.Galardon, M.Giorgi, and I.Artaud (2005).
Direct synthesis of a thiolato-S and sulfinato-S Co(III) complex related to the active site of nitrile hydratase: a pathway to the post-translational oxidation of the protein.
  Angew Chem Int Ed Engl, 44, 6162-6165.  
15696588 M.V.Rampersad, S.P.Jeffery, J.H.Reibenspies, C.G.Ortiz, D.J.Darensbourg, and M.Y.Darensbourg (2005).
N2S2Ni metallothiolates as a class of ligands that support organometallic and bioorganometallic reactivity.
  Angew Chem Int Ed Engl, 44, 1217-1220.  
16097794 S.Rayat, M.Qian, and R.Glaser (2005).
Nitrosative cytosine deamination. An exploration of the chemistry emanating from deamination with pyrimidine ring-opening.
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15764814 T.Buhrke, S.Löscher, O.Lenz, E.Schlodder, I.Zebger, L.K.Andersen, P.Hildebrandt, W.Meyer-Klaucke, H.Dau, B.Friedrich, and M.Haumann (2005).
Reduction of unusual iron-sulfur clusters in the H2-sensing regulatory Ni-Fe hydrogenase from Ralstonia eutropha H16.
  J Biol Chem, 280, 19488-19495.  
14717710 A.Miyanaga, S.Fushinobu, K.Ito, H.Shoun, and T.Wakagi (2004).
Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding.
  Eur J Biochem, 271, 429-438.
PDB codes: 1ugp 1ugq 1ugr 1ugs
15306376 M.Nakasako (2004).
Water-protein interactions from high-resolution protein crystallography.
  Philos Trans R Soc Lond B Biol Sci, 359, 1191.  
12588867 J.A.Lodge, T.Maier, W.Liebl, V.Hoffmann, and N.Sträter (2003).
Crystal structure of Thermotoga maritima alpha-glucosidase AglA defines a new clan of NAD+-dependent glycosidases.
  J Biol Chem, 278, 19151-19158.
PDB code: 1obb
14505323 J.M.Stevens, M.Belghazi, M.Jaouen, D.Bonnet, J.M.Schmitter, D.Mansuy, M.A.Sari, and I.Artaud (2003).
Post-translational modification of Rhodococcus R312 and Comamonas NI1 nitrile hydratases.
  J Mass Spectrom, 38, 955-961.  
14532022 P.F.Brandão, J.P.Clapp, and A.T.Bull (2003).
Diversity of nitrile hydratase and amidase enzyme genes in Rhodococcus erythropolis recovered from geographically distinct habitats.
  Appl Environ Microbiol, 69, 5754-5766.  
14529274 T.Noguchi, M.Nojiri, K.Takei, M.Odaka, and N.Kamiya (2003).
Protonation structures of Cys-sulfinic and Cys-sulfenic acids in the photosensitive nitrile hydratase revealed by Fourier transform infrared spectroscopy.
  Biochemistry, 42, 11642-11650.  
12203518 A.K.Patra, R.Afshar, M.M.Olmstead, and P.K.Mascharak (2002).
The first non-heme iron(III) complex with a ligated carboxamido group that exhibits photolability of a bound NO ligand.
  Angew Chem Int Ed Engl, 41, 2512-2515.  
12386327 T.I.Doukov, T.M.Iverson, J.Seravalli, S.W.Ragsdale, and C.L.Drennan (2002).
A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
  Science, 298, 567-572.
PDB code: 1mjg
11554444 D.E.Wilcox, A.D.Schenk, B.M.Feldman, and Y.Xu (2001).
Oxidation of zinc-binding cysteine residues in transcription factor proteins.
  Antioxid Redox Signal, 3, 549-564.  
11893064 H.Yamada, S.Shimizu, and M.Kobayashi (2001).
Hydratases involved in nitrile conversion: screening, characterization and application.
  Chem Rec, 1, 152-161.  
11698675 L.Xie, and W.A.van der Donk (2001).
Homemade cofactors: self-processing in galactose oxidase.
  Proc Natl Acad Sci U S A, 98, 12863-12865.  
11357946 M.A.Tarnopolsky, and M.F.Beal (2001).
Potential for creatine and other therapies targeting cellular energy dysfunction in neurological disorders.
  Ann Neurol, 49, 561-574.  
10679370 M.Kobayashi, and S.Shimizu (2000).
Nitrile hydrolases.
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10903941 N.M.Okeley, and W.A.van der Donk (2000).
Novel cofactors via post-translational modifications of enzyme active sites.
  Chem Biol, 7, R159-R171.  
  10850812 T.Murakami, M.Nojiri, H.Nakayama, M.Odaka, M.Yohda, N.Dohmae, K.Takio, T.Nagamune, and I.Endo (2000).
Post-translational modification is essential for catalytic activity of nitrile hydratase.
  Protein Sci, 9, 1024-1030.  
10569923 A.Claiborne, J.I.Yeh, T.C.Mallett, J.Luba, E.J.Crane, V.Charrier, and D.Parsonage (1999).
Protein-sulfenic acids: diverse roles for an unlikely player in enzyme catalysis and redox regulation.
  Biochemistry, 38, 15407-15416.  
  10354562 I.Endo, M.Odaka, and M.Yohda (1999).
An enzyme controlled by light: the molecular mechanism of photoreactivity in nitrile hydratase.
  Trends Biotechnol, 17, 244-248.  
10469129 Y.Kato, T.Tsuda, and Y.Asano (1999).
Nitrile hydratase involved in aldoxime metabolism from Rhodococcus sp. strain YH3-3 purification and characterization.
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9702770 M.Kobayashi, and S.Shimizu (1998).
Metalloenzyme nitrile hydratase: structure, regulation, and application to biotechnology.
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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.