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PDBsum entry 1wad

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protein ligands metals links
Electron transport PDB id
1wad
Jmol
Contents
Protein chain
111 a.a. *
Ligands
HEM ×4
Metals
_CA
Waters ×102
* Residue conservation analysis
PDB id:
1wad
Name: Electron transport
Title: Cytochrome c3 with 4 heme groups and one calcium ion
Structure: Cytochrome c3. Chain: a
Source: Desulfovibrio gigas. Organism_taxid: 879
Resolution:
1.80Å     R-factor:   0.149     R-free:   0.219
Authors: P.M.Matias,J.Morais,R.Coelho,M.A.Carrondo,K.Wilson,Z.Dauter, L.Sieker
Key ref: P.M.Matias et al. (1996). Cytochrome c3 from Desulfovibrio gigas: crystal structure at 1.8 A resolution and evidence for a specific calcium-binding site. Protein Sci, 5, 1342-1354. PubMed id: 8819167 DOI: 10.1002/pro.5560050713
Date:
10-Jan-96     Release date:   27-Jan-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00133  (CYC3_DESGI) -  Cytochrome c3
Seq:
Struc:
112 a.a.
111 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     electron carrier activity     3 terms  

 

 
DOI no: 10.1002/pro.5560050713 Protein Sci 5:1342-1354 (1996)
PubMed id: 8819167  
 
 
Cytochrome c3 from Desulfovibrio gigas: crystal structure at 1.8 A resolution and evidence for a specific calcium-binding site.
P.M.Matias, J.Morais, R.Coelho, M.A.Carrondo, K.Wilson, Z.Dauter, L.Sieker.
 
  ABSTRACT  
 
Crystals of the tetraheme cytochrome c3 from sulfate-reducing bacteria Desulfovibrio gigas (Dg) (MW 13 kDa, 111 residues, four heme groups) were obtained and X-ray diffraction data collected to 1.8 A resolution. The structure was solved by the method of molecular replacement and the resulting model refined to a conventional R-factor of 14.9%. The three-dimensional structure shows many similarities to other known crystal structures of tetraheme c3 cytochromes, but it also shows some remarkable differences. In particular, the location of the aromatic residues around the heme groups, which may play a fundamental role in the electron transfer processes of the molecule, are well conserved in the cases of hemes I, III, and IV. However, heme II has an aromatic environment that is completely different to that found in other related cytochromes c3. Another unusual feature is the presence of a Ca2+ ion coordinated by oxygen atoms supplied by the protein within a loop near the N-terminus. It is speculated that this loop may be stabilized by the presence of this Ca2+ ion, may contribute to heme-redox perturbation, and might even be involved in the specificity of recognition with its redox partner.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16964504 R.O.Louro (2007).
Proton thrusters: overview of the structural and functional features of soluble tetrahaem cytochromes c3.
  J Biol Inorg Chem, 12, 1.  
16234915 C.G.Mowat, and S.K.Chapman (2005).
Multi-heme cytochromes--new structures, new chemistry.
  Dalton Trans, (), 3381-3389.  
15764652 L.Rivas, C.M.Soares, A.M.Baptista, J.Simaan, R.E.Di Paolo, D.H.Murgida, and P.Hildebrandt (2005).
Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies.
  Biophys J, 88, 4188-4199.  
14705030 I.Bento, P.M.Matias, A.M.Baptista, P.N.da Costa, W.M.van Dongen, L.M.Saraiva, T.R.Schneider, C.M.Soares, and M.A.Carrondo (2004).
Molecular basis for redox-Bohr and cooperative effects in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies of oxidized and reduced high-resolution structures at pH 7.6.
  Proteins, 54, 135-152.
PDB codes: 1up9 1upd
15133162 P.R.Pokkuluri, Y.Y.Londer, N.E.Duke, J.Erickson, M.Pessanha, C.A.Salgueiro, and M.Schiffer (2004).
Structure of a novel c7-type three-heme cytochrome domain from a multidomain cytochrome c polymer.
  Protein Sci, 13, 1684-1692.
PDB code: 1rwj
15111396 V.H.Teixeira, A.M.Baptista, and C.M.Soares (2004).
Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3).
  Biophys J, 86, 2773-2785.  
12657783 D.Aragão, C.Frazão, L.Sieker, G.M.Sheldrick, J.LeGall, and M.A.Carrondo (2003).
Structure of dimeric cytochrome c3 from Desulfovibrio gigas at 1.2 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 644-653.
PDB code: 1gyo
12012460 A.J.Simaan, D.H.Murgida, and P.Hildebrandt (2002).
Active site structure and dynamics of cytochrome c3 from Desulfovibrio gigas immobilized on electrodes.
  Biopolymers, 67, 331-334.  
11425747 A.I.Tsapin, I.Vandenberghe, K.H.Nealson, J.H.Scott, T.E.Meyer, M.A.Cusanovich, E.Harada, T.Kaizu, H.Akutsu, D.Leys, and J.J.Van Beeumen (2001).
Identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in Shewanella oneidensis strain MR1.
  Appl Environ Microbiol, 67, 3236-3244.  
11948878 F.M.Valente, L.M.Saraiva, J.LeGall, A.V.Xavier, M.Teixeira, and I.A.Pereira (2001).
A membrane-bound cytochrome c3: a type II cytochrome c3 from Desulfovibrio vulgaris Hildenborough.
  Chembiochem, 2, 895-905.  
11320307 M.Czjzek, P.Arnoux, R.Haser, and W.Shepard (2001).
Structure of cytochrome c7 from Desulfuromonas acetoxidans at 1.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 670-678.
PDB code: 1hh5
11358521 O.Einsle, S.Foerster, K.Mann, G.Fritz, A.Messerschmidt, and P.M.Kroneck (2001).
Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from Desulfovibrio desulfuricans Essex 6.
  Eur J Biochem, 268, 3028-3035.
PDB code: 1i77
11425320 S.D.Zarić, D.M.Popović, and E.W.Knapp (2001).
Factors determining the orientation of axially coordinated imidazoles in heme proteins.
  Biochemistry, 40, 7914-7928.  
11170457 S.Umhau, G.Fritz, K.Diederichs, J.Breed, W.Welte, and P.M.Kroneck (2001).
Three-dimensional structure of the nonaheme cytochrome c from Desulfovibrio desulfuricans Essex in the Fe(III) state at 1.89 A resolution.
  Biochemistry, 40, 1308-1316.
PDB code: 1duw
10672013 G.Chottard, I.Kazanskaya, and M.Bruschi (2000).
Resonance Raman study of multihemic c-type cytochromes from Desulfuromonas acetoxidans.
  Eur J Biochem, 267, 1050-1058.  
11004501 P.N.da Costa, P.E.Marujo, W.M.van Dongen, C.M.Arraiano, and L.M.Saraiva (2000).
Cloning, sequencing and expression of the tetraheme cytochrome c(3) from Desulfovibrio gigas.
  Biochim Biophys Acta, 1492, 271-275.  
9890880 A.Dolla, P.Arnoux, I.Protasevich, V.Lobachov, M.Brugna, M.T.Giudici-Orticoni, R.Haser, M.Czjzek, A.Makarov, and M.Bruschi (1999).
Key role of phenylalanine 20 in cytochrome c3: structure, stability, and function studies.
  Biochemistry, 38, 33-41.
PDB code: 1mdv
10354425 A.M.Baptista, P.J.Martel, and C.M.Soares (1999).
Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.
  Biophys J, 76, 2978-2998.  
10561607 M.Assfalg, L.Banci, I.Bertini, M.Bruschi, M.T.Giudici-Orticoni, and P.Turano (1999).
A proton-NMR investigation of the fully reduced cytochrome c7 from Desulfuromonas acetoxidans. Comparison between the reduced and the oxidized forms.
  Eur J Biochem, 266, 634-643.
PDB codes: 1ehj 1f22
9545034 C.M.Soares, P.J.Martel, J.Mendes, and M.A.Carrondo (1998).
Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.
  Biophys J, 74, 1708-1721.  
9730815 J.G.Ma, J.Zhang, R.Franco, S.L.Jia, I.Moura, J.J.Moura, P.M.Kroneck, and J.A.Shelnutt (1998).
The structural origin of nonplanar heme distortions in tetraheme ferricytochromes c3.
  Biochemistry, 37, 12431-12442.  
9843386 R.O.Louro, T.Catarino, D.L.Turner, M.A.Piçarra-Pereira, I.Pacheco, J.LeGall, and A.V.Xavier (1998).
Functional and mechanistic studies of cytochrome c3 from Desulfovibrio gigas: thermodynamics of a "proton thruster".
  Biochemistry, 37, 15808-15815.  
9726950 T.Ohmura, H.Nakamura, K.Niki, M.A.Cusanovich, and H.Akutsu (1998).
Ionic strength-dependent physicochemical factors in cytochrome c3 regulating the electron transfer rate.
  Biophys J, 75, 1483-1490.  
9533688 W.Jentzen, J.G.Ma, and J.A.Shelnutt (1998).
Conservation of the conformation of the porphyrin macrocycle in hemoproteins.
  Biophys J, 74, 753-763.  
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.