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PDBsum entry 1fcd
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Electron transport(flavocytochrome) PDB id
1fcd

 

 

 

 

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Contents
Protein chains
401 a.a. *
174 a.a. *
Ligands
FAD ×2
HEC ×4
* Residue conservation analysis
PDB id:
1fcd
Name: Electron transport(flavocytochrome)
Title: The structure of flavocytochromE C sulfide dehydrogenase from a purple phototrophic bacterium chromatium vinosum at 2.5 angstroms resolution
Structure: FlavocytochromE C sulfide dehydrogenase (flavin-binding subunit). Chain: a, b. Engineered: yes. FlavocytochromE C sulfide dehydrogenase (cytochrome subunit). Chain: c, d. Engineered: yes
Source: Allochromatium vinosum. Organism_taxid: 1049. Organism_taxid: 1049
Biol. unit: Dimer (from PQS)
Resolution:
2.53Å     R-factor:   0.237    
Authors: Z.W.Chen,M.Koh,G.Van Driessche,J.J.Van Beeumen,R.G.Bartsch,T.E.Meyer, M.A.Cusanovich,F.S.Mathews
Key ref: Z.W.Chen et al. (1994). The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium. Science, 266, 430-432. PubMed id: 7939681 DOI: 10.1126/science.7939681
Date:
18-Aug-94     Release date:   01-Nov-94    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q06530  (DHSU_ALLVD) -  Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)
Seq:
Struc: 		431 a.a.
401 a.a.*
Protein chains
Pfam   ArchSchema ?
Q06529  (CYSD_ALLVD) -  Cytochrome subunit of sulfide dehydrogenase from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)
Seq:
Struc: 		199 a.a.
174 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.1.8.2.3  - sulfide-cytochrome-c reductase (flavocytochrome c).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: hydrogen sulfide + 2 Fe(III)-[cytochrome c] = sulfur + 2 Fe(II)- [cytochrome c] + H+
Hydrogen sulfide
 + 2 × ferricytochrome c
 = sulfur
 + 2 × ferrocytochrome c
      Cofactor: FAD; Heme c
FAD
Bound ligand (Het Group name = FAD) corresponds exactly 		Heme c
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1126/science.7939681 Science 266:430-432 (1994)
PubMed id: 7939681  
 
 
The structure of flavocytochrome c sulfide dehydrogenase from a purple phototrophic bacterium.
Z.W.Chen, M.Koh, G.Van Driessche, J.J.Van Beeumen, R.G.Bartsch, T.E.Meyer, M.A.Cusanovich, F.S.Mathews.
 
  ABSTRACT  
 
The structure of the heterodimeric flavocytochrome c sulfide dehydrogenase from Chromatium vinosum was determined at a resolution of 2.53 angstroms. It contains a glutathione reductase-like flavin-binding subunit and a diheme cytochrome subunit. The diheme cytochrome folds as two domains, each resembling mitochondrial cytochrome c, and has an unusual interpropionic acid linkage joining the two heme groups in the interior of the subunit. The active site of the flavoprotein subunit contains a catalytically important disulfide bridge located above the pyrimidine portion of the flavin ring. A tryptophan, threonine, or tyrosine side chain may provide a partial conduit for electron transfer to one of the heme groups located 10 angstroms from the flavin.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20077566 M.Marcia, U.Ermler, G.Peng, and H.Michel (2010).
A new structure-based classification of sulfide:quinone oxidoreductases.
  Proteins, 78, 1073-1083.  
19438712 D.P.Heuts, N.S.Scrutton, W.S.McIntire, and M.W.Fraaije (2009).
What's in a covalent bond? On the role and formation of covalently bound flavin cofactors.
  FEBS J, 276, 3405-3427.  
19725515 J.R.Wallen, T.C.Mallett, W.Boles, D.Parsonage, C.M.Furdui, P.A.Karplus, and A.Claiborne (2009).
Crystal structure and catalytic properties of Bacillus anthracis CoADR-RHD: implications for flavin-linked sulfur trafficking.
  Biochemistry, 48, 9650-9667.
PDB codes: 3icr 3ics 3ict
19028893 L.K.Chan, R.M.Morgan-Kiss, and T.E.Hanson (2009).
Functional analysis of three sulfide:quinone oxidoreductase homologs in Chlorobaculum tepidum.
  J Bacteriol, 191, 1026-1034.  
19487671 M.Marcia, U.Ermler, G.Peng, and H.Michel (2009).
The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.
  Proc Natl Acad Sci U S A, 106, 9625-9630.
PDB codes: 3h27 3h28 3h29 3hyv 3hyw 3hyx
  16880567 I.Tomcová, R.M.Branca, G.Bodó, C.Bagyinka, and I.K.Smatanová (2006).
Cross-crystallization method used for the crystallization and preliminary diffraction analysis of a novel di-haem cytochrome c4.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 820-824.  
15798972 R.E.Galian, L.Pastor-Pérez, M.A.Miranda, and J.Pérez-Prieto (2005).
Intramolecular electron transfer between tyrosine and tryptophan photosensitized by a chiral pi,pi* aromatic ketone.
  Chemistry, 11, 3443-3448.  
11939777 A.Brigé, D.Leys, T.E.Meyer, M.A.Cusanovich, and J.J.Van Beeumen (2002).
The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
  Biochemistry, 41, 4827-4836.
PDB code: 1jni
12151227 A.E.Todd, C.A.Orengo, and J.M.Thornton (2002).
Plasticity of enzyme active sites.
  Trends Biochem Sci, 27, 419-426.  
12411478 V.A.Bamford, S.Bruno, T.Rasmussen, C.Appia-Ayme, M.R.Cheesman, B.C.Berks, and A.M.Hemmings (2002).
Structural basis for the oxidation of thiosulfate by a sulfur cycle enzyme.
  EMBO J, 21, 5599-5610.
PDB codes: 1h31 1h32 1h33
12057198 Z.W.Chen, K.Matsushita, T.Yamashita, T.A.Fujii, H.Toyama, O.Adachi, H.D.Bellamy, and F.S.Mathews (2002).
Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5.
  Structure, 10, 837-849.
PDB code: 1kv9
11567011 C.Appia-Ayme, P.J.Little, Y.Matsumoto, A.P.Leech, and B.C.Berks (2001).
Cytochrome complex essential for photosynthetic oxidation of both thiosulfate and sulfide in Rhodovulum sulfidophilum.
  J Bacteriol, 183, 6107-6118.  
11761328 D.E.Edmondson, and P.Newton-Vinson (2001).
The covalent FAD of monoamine oxidase: structural and functional role and mechanism of the flavinylation reaction.
  Antioxid Redox Signal, 3, 789-806.  
11455601 K.A.Denessiouk, V.V.Rantanen, and M.S.Johnson (2001).
Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins.
  Proteins, 44, 282-291.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
10673428 B.M.Hallberg, T.Bergfors, K.Bäckbro, G.Pettersson, G.Henriksson, and C.Divne (2000).
A new scaffold for binding haem in the cytochrome domain of the extracellular flavocytochrome cellobiose dehydrogenase.
  Structure, 8, 79-88.
PDB codes: 1d7b 1d7c 1d7d
10692367 D.J.Studholme, S.R.Wigneshwereraraj, M.T.Gallegos, and M.Buck (2000).
Functionality of purified sigma(N) (sigma(54)) and a NifA-like protein from the hyperthermophile Aquifex aeolicus.
  J Bacteriol, 182, 1616-1623.  
10852862 M.Bronstein, M.Schütz, G.Hauska, E.Padan, and Y.Shahak (2000).
Cyanobacterial sulfide-quinone reductase: cloning and heterologous expression.
  J Bacteriol, 182, 3336-3344.  
10651042 O.Vallon (2000).
New sequence motifs in flavoproteins: evidence for common ancestry and tools to predict structure.
  Proteins, 38, 95.  
10894738 P.N.Mukhopadhyaya, C.Deb, C.Lahiri, and P.Roy (2000).
A soxA gene, encoding a diheme cytochrome c, and a sox locus, essential for sulfur oxidation in a new sulfur lithotrophic bacterium.
  J Bacteriol, 182, 4278-4287.  
10809687 V.Kostanjevecki, A.Brigé, T.E.Meyer, M.A.Cusanovich, Y.Guisez, and J.van Beeumen (2000).
A membrane-bound flavocytochrome c-sulfide dehydrogenase from the purple phototrophic sulfur bacterium Ectothiorhodospira vacuolata.
  J Bacteriol, 182, 3097-3103.  
10425677 A.Mattevi, G.Tedeschi, L.Bacchella, A.Coda, A.Negri, and S.Ronchi (1999).
Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family.
  Structure, 7, 745-756.
PDB code: 1chu
10368302 P.Trickey, M.A.Wagner, M.S.Jorns, and F.S.Mathews (1999).
Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
  Structure, 7, 331-345.
PDB codes: 1b3m 1l9f 2gb0
  9514256 M.Mewies, W.S.McIntire, and N.S.Scrutton (1998).
Covalent attachment of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) to enzymes: the current state of affairs.
  Protein Sci, 7, 7.  
9032080 A.Kadziola, and S.Larsen (1997).
Crystal structure of the dihaem cytochrome c4 from Pseudomonas stutzeri determined at 2.2A resolution.
  Structure, 5, 203-216.
PDB code: 1etp
9346301 B.Devreese, C.Costa, H.Demol, V.Papaefthymiou, I.Moura, J.J.Moura, and J.Van Beeumen (1997).
The primary structure of the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774 reveals an unusual type of diheme cytochrome c.
  Eur J Biochem, 248, 445-451.  
  9260941 C.Wodara, F.Bardischewsky, and C.G.Friedrich (1997).
Cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of Paracoccus denitrificans GB17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation.
  J Bacteriol, 179, 5014-5023.  
  8880899 G.Van Driessche, M.Koh, Z.W.Chen, F.S.Mathews, T.E.Meyer, R.G.Bartsch, M.A.Cusanovich, and J.J.Van Beeumen (1996).
Covalent structure of the flavoprotein subunit of the flavocytochrome c: sulfide dehydrogenase from the purple phototrophic bacterium Chromatium vinosum.
  Protein Sci, 5, 1753-1764.  
7588806 M.T.Bes, A.L.De Lacey, M.L.Peleato, V.M.Fernandez, and C.Gómez-Moreno (1995).
The covalent linkage of a viologen to a flavoprotein reductase transforms it into an oxidase.
  Eur J Biochem, 233, 593-599.  
  8557026 U.Ermler, R.A.Siddiqui, R.Cramm, and B.Friedrich (1995).
Crystal structure of the flavohemoglobin from Alcaligenes eutrophus at 1.75 A resolution.
  EMBO J, 14, 6067-6077.
PDB code: 1cqx
8591033 V.Fülöp, C.J.Ridout, C.Greenwood, and J.Hajdu (1995).
Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa.
  Structure, 3, 1225-1233.
PDB code: 1eb7
8847342 W.B.Curry, M.D.Grabe, I.V.Kurnikov, S.S.Skourtis, D.N.Beratan, J.J.Regan, A.J.Aquino, P.Beroza, and J.N.Onuchic (1995).
Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins.
  J Bioenerg Biomembr, 27, 285-293.  
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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