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PDBsum entry 1ahj

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protein metals Protein-protein interface(s) links
Lyase PDB id
1ahj
Jmol
Contents
Protein chains
198 a.a. *
212 a.a. *
Metals
_FE ×4
* Residue conservation analysis
PDB id:
1ahj
Name: Lyase
Title: Nitrile hydratase
Structure: Nitrile hydratase (subunit alpha). Chain: a, c, e, g. Nitrile hydratase (subunit beta). Chain: b, d, f, h. Ec: 4.2.1.84
Source: Rhodococcus sp. R312. Organism_taxid: 76275. Organism_taxid: 76275
Biol. unit: Hetero-Dimer (from PDB file)
Resolution:
2.65Å     R-factor:   0.264     R-free:   0.289
Authors: W.Huang,G.Schneider,Y.Lindqvist
Key ref:
W.Huang et al. (1997). Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold. Structure, 5, 691-699. PubMed id: 9195885 DOI: 10.1016/S0969-2126(97)00223-2
Date:
05-Apr-97     Release date:   08-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P13448  (NHAA_RHOER) -  Nitrile hydratase subunit alpha
Seq:
Struc:
207 a.a.
198 a.a.*
Protein chains
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 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F, G, H: 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!
  Biological process     nitrogen compound metabolic process   1 term 
  Biochemical function     catalytic activity     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0969-2126(97)00223-2 Structure 5:691-699 (1997)
PubMed id: 9195885  
 
 
Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold.
W.Huang, J.Jia, J.Cummings, M.Nelson, G.Schneider, Y.Lindqvist.
 
  ABSTRACT  
 
BACKGROUND: Nitrile hydratases are unusual metalloenzymes that catalyze the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alphabeta unit. We have determined the crystal structure of photoactivated iron-containing nitrile hydratase from Rhodococcus sp. R312 to 2.65 A resolution as a first step in the elucidation of its catalytic mechanism. RESULTS: The alpha subunit consists of a long N-terminal arm and a C-terminal domain that forms a novel fold. This fold can be described as a four layered structure, alpha-beta-beta-alpha, with unusual connectivities between the beta strands. The beta subunit also contains a long N-terminal extension, a helical domain, and a C-terminal domain that folds into a beta roll. The two subunits form a tight heterodimer that is the functional unit of the enzyme. The active site is located in a cavity at the subunit-subunit interface. The iron centre is formed by residues from the alpha subunit only-three cysteine thiolates and two mainchain amide nitrogen atoms are ligands. CONCLUSIONS: Nitrile hydratases contain a novel iron centre with a structure not previously observed in proteins; it resembles a hybrid of the iron centres of heme and Fe-S proteins. The low-spin electronic configuration presumably results in part from two Fe-amide nitrogen bonds. The structure is consistent with the metal ion having a role as a Lewis acid in the catalytic reaction.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Subunit topology and structure of nitrile hydratase. (a) Topology diagram for the a and b subunits of nitrile hydratase. The a subunit is shown in blue and the b subunit in yellow. The location of the iron centre is indicated by a red sphere. (b) Schematic view of the a subunit. (c) Schematic view of the b subunit. Figures (b) and (c) were generated with the programs Molscript [36] and Raster3D [37].
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 691-699) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22002607 Y.Shomura, K.S.Yoon, H.Nishihara, and Y.Higuchi (2011).
Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase.
  Nature, 479, 253-256.
PDB codes: 3ayx 3ayy 3ayz
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.
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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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19156270 R.Wang, M.A.Camacho-Fernandez, W.Xu, J.Zhang, and L.Li (2009).
Neutral and reduced Roussin's red salt ester [Fe(2)(mu-RS)(2)(NO)(4)] (R = n-Pr, t-Bu, 6-methyl-2-pyridyl and 4,6-dimethyl-2-pyrimidyl): synthesis, X-ray crystal structures, spectroscopic, electrochemical and density functional theoretical investigations.
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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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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.
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19096720 K.U.Foerstner, T.Doerks, J.Muller, J.Raes, and P.Bork (2008).
A nitrile hydratase in the eukaryote Monosiga brevicollis.
  PLoS ONE, 3, e3976.  
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Photoactive Ruthenium Nitrosyls: Effects of Light and Potential Application as NO Donors.
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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.  
17698201 B.W.Smucker, M.J.Vanstipdonk, and D.M.Eichhorn (2007).
Incorporation of thiolate donation using 2,2'-dithiodibenzaldehyde: complexes of a pentadentate N2S3 ligand with relevance to the active site of Co nitrile hydratase.
  J Inorg Biochem, 101, 1537-1542.  
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.
  Proteins, 69, 665-671.
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.
  J Mol Model, 13, 725-730.  
17330219 L.Song, M.Wang, X.Yang, and S.Qian (2007).
Purification and characterization of the enantioselective nitrile hydratase from Rhodococcus sp. AJ270.
  Biotechnol J, 2, 717-724.  
17150969 S.Mitra, and R.C.Holz (2007).
Unraveling the catalytic mechanism of nitrile hydratases.
  J Biol Chem, 282, 7397-7404.  
16807974 E.I.Solomon, S.I.Gorelsky, and A.Dey (2006).
Metal-thiolate bonds in bioinorganic chemistry.
  J Comput Chem, 27, 1415-1428.  
16584884 H.Alonso, and J.E.Gready (2006).
Integron-sequestered dihydrofolate reductase: a recently redeployed enzyme.
  Trends Microbiol, 14, 236-242.  
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
17193242 R.Singh, R.Sharma, N.Tewari, and D.S.Rawat (2006).
Nitrilase and its application as a 'green' catalyst.
  Chem Biodivers, 3, 1279-1287.  
  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.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 999.  
15803334 A.Volbeda, L.Martin, C.Cavazza, M.Matho, B.W.Faber, W.Roseboom, S.P.Albracht, E.Garcin, M.Rousset, and J.C.Fontecilla-Camps (2005).
Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
  J Biol Inorg Chem, 10, 239-249.
PDB codes: 1yq9 1yqw 1yrq
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.
  Chem Res Toxicol, 18, 1211-1218.  
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
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.
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12948779 P.D.Barker (2003).
Designing redox metalloproteins from bottom-up and top-down perspectives.
  Curr Opin Struct Biol, 13, 490-499.  
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.  
12089004 S.Trott, S.Bürger, C.Calaminus, and A.Stolz (2002).
Cloning and heterologous expression of an enantioselective amidase from Rhodococcus erythropolis strain MP50.
  Appl Environ Microbiol, 68, 3279-3286.  
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
  11380987 H.C.Pace, and C.Brenner (2001).
The nitrilase superfamily: classification, structure and function.
  Genome Biol, 2, REVIEWS0001.  
11893064 H.Yamada, S.Shimizu, and M.Kobayashi (2001).
Hydratases involved in nitrile conversion: screening, characterization and application.
  Chem Rec, 1, 152-161.  
11782293 V.Agrawal, and R.K.Kishan (2001).
Functional evolution of two subtly different (similar) folds.
  BMC Struct Biol, 1, 5.  
10679370 M.Kobayashi, and S.Shimizu (2000).
Nitrile hydrolases.
  Curr Opin Chem Biol, 4, 95.  
  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.  
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.  
10563820 J.L.Zimmermann, T.Amano, and C.Sigalat (1999).
Identification and characterization of Mg2+ binding sites in isolated alpha and beta subunits of H(+)-ATPase from Bacillus PS3.
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10103026 M.Kobayashi, and S.Shimizu (1999).
Cobalt proteins.
  Eur J Biochem, 261, 1-9.  
10209297 R.A.Cramp, and D.A.Cowan (1999).
Molecular characterisation of a novel thermophilic nitrile hydratase.
  Biochim Biophys Acta, 1431, 249-260.  
10336376 R.Schleif (1999).
Arm-domain interactions in proteins: a review.
  Proteins, 34, 1-3.  
10469129 Y.Kato, T.Tsuda, and Y.Asano (1999).
Nitrile hydratase involved in aldoxime metabolism from Rhodococcus sp. strain YH3-3 purification and characterization.
  Eur J Biochem, 263, 662-670.  
9399878 K.N.Degtyarenko, A.C.North, D.N.Perkins, and J.B.Findlay (1998).
PROMISE: a database of information on prosthetic centres and metal ions in protein active sites.
  Nucleic Acids Res, 26, 376-381.  
9702770 M.Kobayashi, and S.Shimizu (1998).
Metalloenzyme nitrile hydratase: structure, regulation, and application to biotechnology.
  Nat Biotechnol, 16, 733-736.  
9622501 M.Merkx, and B.A.Averill (1998).
Ga3+ as a functional substitute for Fe3+: preparation and characterization of the Ga3+Fe2+ and Ga3+Zn2+ forms of bovine spleen purple acid phosphatase.
  Biochemistry, 37, 8490-8497.  
9586994 S.Nagashima, M.Nakasako, N.Dohmae, M.Tsujimura, K.Takio, M.Odaka, M.Yohda, N.Kamiya, and I.Endo (1998).
Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms.
  Nat Struct Biol, 5, 347-351.
PDB code: 2ahj
9914255 U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, and R.K.Thauer (1998).
Active sites of transition-metal enzymes with a focus on nickel.
  Curr Opin Struct Biol, 8, 749-758.  
9698385 W.N.Lanzilotta, J.Christiansen, D.R.Dean, and L.C.Seefeldt (1998).
Evidence for coupled electron and proton transfer in the [8Fe-7S] cluster of nitrogenase.
  Biochemistry, 37, 11376-11384.  
9368004 M.Tsujimura, N.Dohmae, M.Odaka, M.Chijimatsu, K.Takio, M.Yohda, M.Hoshino, S.Nagashima, and I.Endo (1997).
Structure of the photoreactive iron center of the nitrile hydratase from Rhodococcus sp. N-771. Evidence of a novel post-translational modification in the cysteine ligand.
  J Biol Chem, 272, 29454-29459.  
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.