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Oxidoreductase PDB id
1b25
Jmol
Contents
Protein chains
611 a.a. *
Ligands
SF4 ×4
PTT ×4
Waters ×1349
* Residue conservation analysis
PDB id:
1b25
Name: Oxidoreductase
Title: Formaldehyde ferredoxin oxidoreductase from pyrococcus furio
Structure: Protein (formaldehyde ferredoxin oxidoreductase). Chain: a, b, c, d. Fragment: domain 1: 1-208, domain 2: 209-406, domain 3: 407
Source: Pyrococcus furiosus. Organism_taxid: 2261. Atcc: dsm 3638. Collection: dsm 3638
Biol. unit: Homo-Tetramer (from PDB file)
Resolution:
1.85Å     R-factor:   0.174     R-free:   0.220
Authors: Y.L.Hu,S.Faham,R.Roy,M.W.W.Adams,D.C.Rees
Key ref:
Y.Hu et al. (1999). Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications. J Mol Biol, 286, 899-914. PubMed id: 10024458 DOI: 10.1006/jmbi.1998.2488
Date:
04-Dec-98     Release date:   24-Mar-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8U1K3  (Q8U1K3_PYRFU) -  Formaldehyde:ferredoxin oxidoreductase
Seq:
Struc: 		 
Seq:
Struc: 		627 a.a.
611 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     electron carrier activity     6 terms  

 

 
DOI no: 10.1006/jmbi.1998.2488 J Mol Biol 286:899-914 (1999)
PubMed id: 10024458  
 
 
Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications.
Y.Hu, S.Faham, R.Roy, M.W.Adams, D.C.Rees.
 
  ABSTRACT  
 
Crystal structures of formaldehyde ferredoxin oxidoreductase (FOR), a tungstopterin-containing protein from the hyperthermophilic archaeon Pyrococcus furiosus, have been determined in the native state and as a complex with the inhibitor glutarate at 1.85 A and 2. 4 A resolution, respectively. The native structure was solved by molecular replacement using the structure of the homologous P. furiosus aldehyde ferredoxin oxidoreductase (AOR) as the initial model. Residues are identified in FOR that may be involved in either the catalytic mechanism or in determining substrate specificity. The binding site on FOR for the physiological electron acceptor, P. furiosus ferredoxin (Fd), has been established from an FOR-Fd cocrystal structure. Based on the arrangement of redox centers in this structure, an electron transfer pathway is proposed that begins at the tungsten center, leads to the (4Fe:4S) cluster of FOR via one of the two pterins that coordinate the tungsten, and ends at the (4Fe:4S) cluster of ferredoxin. This pathway includes two residues that coordinate the (4Fe:4S) clusters, Cys287 of FOR and Asp14 of ferredoxin. Similarities in the active site structures between FOR and the unrelated molybdoenzyme aldehyde oxidoreductase from Desulfovibrio gigas suggest that both enzymes utilize a common mechanism for aldehyde oxidation.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. The active site cavity of FOR, as defined with the program VOIDOO, with surrounding residues and superimposed glutarate molecule.
Figure 10.
Figure 10. Superposition of the active sites of Mop (cyan; PDB entry 1ALO) and FOR (ball-and-stick model), illustrating the correspondence between active sites and bound ligands (iso-propanol of Mop and glutarate of FOR). The oxygen atoms of the bound water molecules and iso-propanol of Mop are shown as balls.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 286, 899-914) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
21530474 R.Z.Liao, J.G.Yu, and F.Himo (2011).
Tungsten-dependent formaldehyde ferredoxin oxidoreductase: Reaction mechanism from quantum chemical calculations.
  J Inorg Biochem, 105, 927-936.  
19815533 J.W.Kung, C.Löffler, K.Dörner, D.Heintz, S.Gallien, A.Van Dorsselaer, T.Friedrich, and M.Boll (2009).
Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases.
  Proc Natl Acad Sci U S A, 106, 17687-17692.  
17899221 E.Bol, N.J.Broers, and W.R.Hagen (2008).
A steady-state and pre-steady-state kinetics study of the tungstoenzyme formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus.
  J Biol Inorg Chem, 13, 75-84.  
19006327 E.T.Yukl, M.A.Elbaz, M.M.Nakano, and P.Moënne-Loccoz (2008).
Transcription Factor NsrR from Bacillus subtilis Senses Nitric Oxide with a 4Fe-4S Cluster (†).
  Biochemistry, 47, 13084-13092.  
17578578 J.E.Butler, Q.He, K.P.Nevin, Z.He, J.Zhou, and D.R.Lovley (2007).
Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.
  BMC Genomics, 8, 180.  
16924554 E.Bol, L.E.Bevers, P.L.Hagedoorn, and W.R.Hagen (2006).
Redox chemistry of tungsten and iron-sulfur prosthetic groups in Pyrococcus furiosus formaldehyde ferredoxin oxidoreductase.
  J Biol Inorg Chem, 11, 999.  
16428816 N.Kato, H.Yurimoto, and R.K.Thauer (2006).
The physiological role of the ribulose monophosphate pathway in bacteria and archaea.
  Biosci Biotechnol Biochem, 70, 10-21.  
15702182 C.Schulzke (2005).
Temperature dependent electrochemical investigations of molybdenum and tungsten oxobisdithiolene complexes.
  Dalton Trans, 0, 713-720.  
15901685 I.Orita, H.Yurimoto, R.Hirai, Y.Kawarabayasi, Y.Sakai, and N.Kato (2005).
The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway.
  J Bacteriol, 187, 3636-3642.  
15772818 P.L.Hagedoorn, T.Chen, I.Schröder, S.R.Piersma, S.de Vries, and W.R.Hagen (2005).
Purification and characterization of the tungsten enzyme aldehyde:ferredoxin oxidoreductase from the hyperthermophilic denitrifier Pyrobaculum aerophilum.
  J Biol Inorg Chem, 10, 259-269.  
14686934 D.Rauh, A.Graentzdoerffer, K.Granderath, J.R.Andreesen, and A.Pich (2004).
Tungsten-containing aldehyde oxidoreductase of Eubacterium acidaminophilum.
  Eur J Biochem, 271, 212-219.  
12114025 R.Hille (2002).
Molybdenum and tungsten in biology.
  Trends Biochem Sci, 27, 360-367.  
12446645 R.Roy, and M.W.Adams (2002).
Characterization of a fourth tungsten-containing enzyme from the hyperthermophilic archaeon Pyrococcus furiosus.
  J Bacteriol, 184, 6952-6956.  
10985771 R.C.Bray, B.Adams, A.T.Smith, B.Bennett, and S.Bailey (2000).
Reversible dissociation of thiolate ligands from molybdenum in an enzyme of the dimethyl sulfoxide reductase family.
  Biochemistry, 39, 11258-11269.
PDB codes: 1e5v 1e60 1e61
10491097 L.Pieulle, M.H.Charon, P.Bianco, J.Bonicel, Y.Pétillot, and E.C.Hatchikian (1999).
Structural and kinetic studies of the pyruvate-ferredoxin oxidoreductase/ferredoxin complex from Desulfovibrio africanus.
  Eur J Biochem, 264, 500-508.  
10607667 M.H.Charon, A.Volbeda, E.Chabriere, L.Pieulle, and J.C.Fontecilla-Camps (1999).
Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase.
  Curr Opin Struct Biol, 9, 663-669.  
10387062 P.L.Wang, L.Calzolai, K.L.Bren, Q.Teng, F.E.Jenney, P.S.Brereton, J.B.Howard, M.W.Adams, and G.N.La Mar (1999).
Secondary structure extensions in Pyrococcus furiosus ferredoxin destabilize the disulfide bond relative to that in other hyperthermostable ferredoxins. Global consequences for the disulfide orientational heterogeneity.
  Biochemistry, 38, 8167-8178.  
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.