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PDBsum entry 1c4c
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Oxidoreductase PDB id
1c4c

 

 

 

 

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Contents
Protein chain
574 a.a. *
Ligands
HC0
SF4 ×4
FES
Waters ×314
* Residue conservation analysis
PDB id:
1c4c
Name: Oxidoreductase
Title: Binding of exogenously added carbon monoxide at the active site of the fe-only hydrogenase (cpi) from clostridium pasteurianum
Structure: Protein (fe-only hydrogenase). Chain: a. Synonym: cpi. Ec: 1.18.99.1
Source: Clostridium pasteurianum. Organism_taxid: 1501. Cellular_location: cytoplasm
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.193     R-free:   0.240
Authors: B.J.Lemon,J.W.Peters
Key ref:
B.J.Lemon and J.W.Peters (1999). Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum. Biochemistry, 38, 12969-12973. PubMed id: 10529166 DOI: 10.1021/bi9913193
Date:
16-Aug-99     Release date:   22-Dec-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29166  (PHF1_CLOPA) -  Iron hydrogenase 1 from Clostridium pasteurianum
Seq:
Struc: 		 
Seq:
Struc: 		574 a.a.
574 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.12.7.2  - ferredoxin hydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 reduced [2Fe-2S]-[ferredoxin] + 2 H+
      Cofactor: Iron-sulfur; Ni(2+)
Iron-sulfur
 Ni(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1021/bi9913193 Biochemistry 38:12969-12973 (1999)
PubMed id: 10529166  
 
 
Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum.
B.J.Lemon, J.W.Peters.
 
  ABSTRACT  
 
A site for the binding of exogenously added carbon monoxide has been identified at the active site of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum. The binding and inhibition of carbon monoxide have been exploited in biochemical and spectroscopic studies to gain mechanistic insights. In the present study, we have taken advantage of the ability to generate an irreversibly carbon monoxide bound state of CpI. The crystallization and structural characterization of CpI inhibited in the presence of carbon monoxide indicates the addition of a single molecule of carbon monoxide. The ability to generate crystals of the carbon monoxide bound state of the hydrogenase that are isomorphous to those of the native enzyme has allowed for a direct comparison of the crystallographic data and an unambiguous identification of the site of carbon monoxide binding at the active site of CpI. Carbon monoxide binds to an Fe atom of the 2Fe subcluster at the site of a terminally bound water molecule in the as crystallized native state of CpI that has been previously suggested to be a potential site of reversible hydrogen oxidation. Binding of carbon monoxide at this site results in an active site that is coordinately saturated with strong ligands (S, CO, and CN), providing a rational potential mechanism for inhibition of reversible hydrogen oxidation at the active site of CpI.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21063595 S.Lounissi, J.F.Capon, F.Gloaguen, F.Matoussi, F.Y.Pétillon, P.Schollhammer, and J.Talarmin (2011).
Diiron species containing a cyclic P(Ph)2N(Ph)2 diphosphine related to the [FeFe]H2ases active site.
  Chem Commun (Camb), 47, 878-880.  
20593098 C.Greco, P.Fantucci, L.De Gioia, R.Suarez-Bertoa, M.Bruschi, J.Talarmin, and P.Schollhammer (2010).
Electrocatalytic dihydrogen evolution mechanism of [Fe2(CO)4(kappa(2)-Ph2PCH2CH2PPh2)(mu-S(CH2)3S)] and related models of the [FeFe]-hydrogenases active site: a DFT investigation.
  Dalton Trans, 39, 7320-7329.  
20669037 C.Gutiérrez-Sánchez, O.Rüdiger, V.M.Fernández, A.L.De Lacey, M.Marques, and I.A.Pereira (2010).
Interaction of the active site of the Ni-Fe-Se hydrogenase from Desulfovibrio vulgaris Hildenborough with carbon monoxide and oxygen inhibitors.
  J Biol Inorg Chem, 15, 1285-1292.  
20221544 P.Surawatanawong, J.W.Tye, M.Y.Darensbourg, and M.B.Hall (2010).
Mechanism of electrocatalytic hydrogen production by a di-iron model of iron-iron hydrogenase: a density functional theory study of proton dissociation constants and electrode reduction potentials.
  Dalton Trans, 39, 3093-3104.  
  20628586 S.N.Parshina, J.Sipma, A.M.Henstra, and A.J.Stams (2010).
Carbon monoxide as an electron donor for the biological reduction of sulphate.
  Int J Microbiol, 2010, 319527.  
19011912 A.Silakov, B.Wenk, E.Reijerse, S.P.Albracht, and W.Lubitz (2009).
Spin distribution of the H-cluster in the H(ox)-CO state of the [FeFe] hydrogenase from Desulfovibrio desulfuricans: HYSCORE and ENDOR study of (14)N and (13)C nuclear interactions.
  J Biol Inorg Chem, 14, 301-313.  
19675641 J.C.Fontecilla-Camps, P.Amara, C.Cavazza, Y.Nicolet, and A.Volbeda (2009).
Structure-function relationships of anaerobic gas-processing metalloenzymes.
  Nature, 460, 814-822.  
19805068 S.T.Stripp, G.Goldet, C.Brandmayr, O.Sanganas, K.A.Vincent, M.Haumann, F.A.Armstrong, and T.Happe (2009).
How oxygen attacks [FeFe] hydrogenases from photosynthetic organisms.
  Proc Natl Acad Sci U S A, 106, 17331-17336.  
18341276 A.K.Justice, M.J.Nilges, T.B.Rauchfuss, S.R.Wilson, L.De Gioia, and G.Zampella (2008).
Diiron dithiolato carbonyls related to the H(ox)CO state of [FeFe]-hydrogenase.
  J Am Chem Soc, 130, 5293-5301.  
18506239 S.Ezzaher, P.Y.Orain, J.F.Capon, F.Gloaguen, F.Y.Pétillon, T.Roisnel, P.Schollhammer, and J.Talarmin (2008).
First insights into the protonation of dissymetrically disubstituted di-iron azadithiolate models of the [FeFe]H2ases active site.
  Chem Commun (Camb), (), 2547-2549.  
18653896 S.Shima, O.Pilak, S.Vogt, M.Schick, M.S.Stagni, W.Meyer-Klaucke, E.Warkentin, R.K.Thauer, and U.Ermler (2008).
The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site.
  Science, 321, 572-575.
PDB codes: 3daf 3dag
17563784 F.I.Adam, G.Hogarth, I.Richards, and B.E.Sanchez (2007).
Models of the iron-only hydrogenase: structural studies of chelating diphosphine complexes [Fe2(CO)4(micro-pdt)(kappa2P,P'-diphosphine)].
  Dalton Trans, (), 2495-2498.  
17195059 L.E.Nagy, J.E.Meuser, S.Plummer, M.Seibert, M.L.Ghirardi, P.W.King, D.Ahmann, and M.C.Posewitz (2007).
Application of gene-shuffling for the rapid generation of novel [FeFe]-hydrogenase libraries.
  Biotechnol Lett, 29, 421-430.  
17031433 L.Schwartz, J.Ekström, R.Lomoth, and S.Ott (2006).
Dynamic ligation at the first amine-coordinated iron hydrogenase active site mimic.
  Chem Commun (Camb), (), 4206-4208.  
16323020 S.P.Albracht, W.Roseboom, and E.C.Hatchikian (2006).
The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. I. Light sensitivity and magnetic hyperfine interactions as observed by electron paramagnetic resonance.
  J Biol Inorg Chem, 11, 88.  
15667271 J.Cohen, K.Kim, M.Posewitz, M.L.Ghirardi, K.Schulten, M.Seibert, and P.King (2005).
Molecular dynamics and experimental investigation of H(2) and O(2) diffusion in [Fe]-hydrogenase.
  Biochem Soc Trans, 33, 80-82.  
16154089 J.Cohen, K.Kim, P.King, M.Seibert, and K.Schulten (2005).
Finding gas diffusion pathways in proteins: application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects.
  Structure, 13, 1321-1329.  
15782259 J.Han, and D.Coucouvanis (2005).
Synthesis and structure of the organometallic MFe2(mu3-S)2 clusters (M = Mo or Fe).
  Dalton Trans, (), 1234-1240.  
12620841 M.M.Watrous, S.Clark, R.Kutty, S.Huang, F.B.Rudolph, J.B.Hughes, and G.N.Bennett (2003).
2,4,6-trinitrotoluene reduction by an Fe-only hydrogenase in Clostridium acetobutylicum.
  Appl Environ Microbiol, 69, 1542-1547.  
12642671 M.Y.Darensbourg, E.J.Lyon, X.Zhao, and I.P.Georgakaki (2003).
The organometallic active site of [Fe]hydrogenase: models and entatic states.
  Proc Natl Acad Sci U S A, 100, 3683-3688.  
12045096 D.C.Rees (2002).
Great metalloclusters in enzymology.
  Annu Rev Biochem, 71, 221-246.  
11353506 J.D.Lawrence, H.Li, T.B.Rauchfuss, M.Bénard, and M.M.Rohmer (2001).
Diiron Azadithiolates as Models for the Iron-Only Hydrogenase Active Site: Synthesis, Structure, and Stereoelectronics This research was supported by the NIH and the Centre Universitaire et Régional de Ressources Informatiques of ULP and CNRS.
  Angew Chem Int Ed Engl, 40, 1768-1771.  
10858294 B.Bennett, B.J.Lemon, and J.W.Peters (2000).
Reversible carbon monoxide binding and inhibition at the active site of the Fe-only hydrogenase.
  Biochemistry, 39, 7455-7460.  
10607666 J.W.Peters (1999).
Structure and mechanism of iron-only hydrogenases.
  Curr Opin Struct Biol, 9, 670-676.  
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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