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PDBsum entry 3c8y
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protein ligands links
Oxidoreductase PDB id
3c8y

 

 

 

 

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Contents
Protein chain
574 a.a. *
Ligands
HCN
SF4 ×4
FES
GOL ×3
Waters ×667
* Residue conservation analysis
PDB id:
3c8y
Name: Oxidoreductase
Title: 1.39 angstrom crystal structure of fe-only hydrogenase
Structure: Iron hydrogenase 1. Chain: a. Synonym: [fe] hydrogenase, fe-only hydrogenase, cpi. Ec: 1.12.7.2
Source: Clostridium pasteurianum
Resolution:
1.39Å     R-factor:   0.140     R-free:   0.194
Authors: A.S.Pandey,B.J.Lemon,J.W.Peters
Key ref: A.S.Pandey et al. (2008). Dithiomethylether as a ligand in the hydrogenase h-cluster. J Am Chem Soc, 130, 4533-4540. PubMed id: 18324814
Date:
14-Feb-08     Release date:   22-Apr-08    
PROCHECK
Go to PROCHECK summary
 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    
 
 
J Am Chem Soc 130:4533-4540 (2008)
PubMed id: 18324814  
 
 
Dithiomethylether as a ligand in the hydrogenase h-cluster.
A.S.Pandey, T.V.Harris, L.J.Giles, J.W.Peters, R.K.Szilagyi.
 
  ABSTRACT  
 
An X-ray crystallographic refinement of the H-cluster of [FeFe]-hydrogenase from Clostridium pasteurianum has been carried out to close-to atomic resolution and is the highest resolution [FeFe]-hydrogenase presented to date. The 1.39 A, anisotropically refined [FeFe]-hydrogenase structure provides a basis for examining the outstanding issue of the composition of the unique nonprotein dithiolate ligand of the H-cluster. In addition to influencing the electronic structure of the H-cluster, the composition of the ligand has mechanistic implications due to the potential of the bridge-head gamma-group participating in proton transfer during catalysis. In this work, sequential density functional theory optimizations of the dithiolate ligand embedded in a 3.5-3.9 A protein environment provide an unbiased approach to examining the most likely composition of the ligand. Structural, conformational, and energetic considerations indicate a preference for dithiomethylether as an H-cluster ligand and strongly disfavor the dithiomethylammonium as a catalytic base for hydrogen production.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21296047 G.Hong, A.J.Cornish, E.L.Hegg, and R.Pachter (2011).
On understanding proton transfer to the biocatalytic [Fe-Fe](H) sub-cluster in [Fe-Fe]H(2)ases: QM/MM MD simulations.
  Biochim Biophys Acta, 1807, 510-517.  
20830602 A.Grigoropoulos, and R.K.Szilagyi (2010).
Evaluation of biosynthetic pathways for the unique dithiolate ligand of the FeFe hydrogenase H-cluster.
  J Biol Inorg Chem, 15, 1177-1182.  
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.  
20418861 D.W.Mulder, E.S.Boyd, R.Sarma, R.K.Lange, J.A.Endrizzi, J.B.Broderick, and J.W.Peters (2010).
Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG).
  Nature, 465, 248-251.
PDB code: 3lx4
20498089 E.M.Shepard, S.E.McGlynn, A.L.Bueling, C.S.Grady-Smith, S.J.George, M.A.Winslow, S.P.Cramer, J.W.Peters, and J.B.Broderick (2010).
Synthesis of the 2Fe subcluster of the [FeFe]-hydrogenase H cluster on the HydF scaffold.
  Proc Natl Acad Sci U S A, 107, 10448-10453.  
20221542 H.Seino, Y.Misumi, Y.Hojo, and Y.Mizobe (2010).
Heterolytic H2 activation by rhodium thiolato complexes bearing the hydrotris(pyrazolyl)borato ligand and application to catalytic hydrogenation under mild conditions.
  Dalton Trans, 39, 3072-3082.  
20221533 J.Y.Yang, R.M.Bullock, W.G.Dougherty, W.S.Kassel, B.Twamley, D.L.DuBois, and M.Rakowski DuBois (2010).
Reduction of oxygen catalyzed by nickel diphosphine complexes with positioned pendant amines.
  Dalton Trans, 39, 3001-3010.  
20225804 M.G.Galinato, C.M.Whaley, and N.Lehnert (2010).
Vibrational analysis of the model complex (mu-edt)[Fe(CO)(3)](2) and comparison to iron-only hydrogenase: the activation scale of hydrogenase model systems.
  Inorg Chem, 49, 3201-3215.  
20235826 R.K.Thauer, A.K.Kaster, M.Goenrich, M.Schick, T.Hiromoto, and S.Shima (2010).
Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage.
  Annu Rev Biochem, 79, 507-536.  
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.  
19639134 A.Silakov, B.Wenk, E.Reijerse, and W.Lubitz (2009).
(14)N HYSCORE investigation of the H-cluster of [FeFe] hydrogenase: evidence for a nitrogen in the dithiol bridge.
  Phys Chem Chem Phys, 11, 6592-6599.  
19088969 F.Gloaguen, and T.B.Rauchfuss (2009).
Small molecule mimics of hydrogenases: hydrides and redox.
  Chem Soc Rev, 38, 100-108.  
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.  
19088964 M.L.Ghirardi, A.Dubini, J.Yu, and P.C.Maness (2009).
Photobiological hydrogen-producing systems.
  Chem Soc Rev, 38, 52-61.  
19575350 R.J.Wright, C.Lim, and T.D.Tilley (2009).
Diiron proton reduction catalysts possessing electron-rich and electron-poor naphthalene-1,8-dithiolate ligands.
  Chemistry, 15, 8518-8525.  
19206188 S.Groysman, and R.H.Holm (2009).
Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites.
  Biochemistry, 48, 2310-2320.  
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.  
19333494 W.G.Wang, H.Y.Wang, G.Si, C.H.Tung, and L.Z.Wu (2009).
Fluorophenyl-substituted Fe-only hydrogenases active site ADT models: different electrocatalytic process for proton reduction in HOAc and HBF4/Et2O.
  Dalton Trans, (), 2712-2720.  
18620387 A.K.Justice, L.De Gioia, M.J.Nilges, T.B.Rauchfuss, S.R.Wilson, and G.Zampella (2008).
Redox and structural properties of mixed-valence models for the active site of the [FeFe]-hydrogenase: progress and challenges.
  Inorg Chem, 47, 7405-7414.  
19053433 B.E.Barton, M.T.Olsen, and T.B.Rauchfuss (2008).
Aza- and oxadithiolates are probable proton relays in functional models for the [FeFe]-hydrogenases.
  J Am Chem Soc, 130, 16834-16835.  
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 code is shown on the right.

 

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