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PDBsum entry 155c
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Electron transport PDB id
155c

 

 

 

 

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Contents
Protein chain
135 a.a. *
Ligands
HEM
* Residue conservation analysis
PDB id:
155c
Name: Electron transport
Title: The structure of paracoccus denitrificans cytochrome c550
Structure: Cytochrome c550. Chain: a. Engineered: yes
Source: Paracoccus denitrificans. Micrococcus denitrificans. Organism_taxid: 266
Resolution:
2.50Å     R-factor:   not given    
Authors: R.Timkovich
Key ref: R.Timkovich and R.E.Dickerson (1976). The structure of Paracoccus denitrificans cytochrome c550. J Biol Chem, 251, 4033-4046. PubMed id: 180013
Date:
01-Aug-76     Release date:   20-Aug-76    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00096  (CY550_PARDE) -  Cytochrome c-550 from Paracoccus denitrificans
Seq:
Struc: 		155 a.a.
134 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 21 residue positions (black crosses)

 

 
J Biol Chem 251:4033-4046 (1976)
PubMed id: 180013  
 
 
The structure of Paracoccus denitrificans cytochrome c550.
R.Timkovich, R.E.Dickerson.
 
  ABSTRACT  
 
The crystal structure of Paracoccus (formerly Micrococcus) denitrificans cytochrome c550 has been solved by x-ray diffraction to a resolution of 2.45 A. In both amino acid sequence and molecular structure it is evolutionarily homologous with mitochondrial cytochrome c from eukaryotes and photosynthetic cytochrome c2 from purple non-sulfur bacteria. All of these cytochromes c have the same basic folding pattern, with surface insertions of extra amino acids in c550. Various strains of c2 have all, some, or none of the extra insertions observed in c550. The hydrophobic heme environment, position of aromatic rings, and structure and environment of the heme crevice, are virtually identical in cytochromes c55o, c, and c2. Radical changes observed at all regions on the molecular surface except the heme crevice argue for the importance of the crevice and the exposed edge of the heme in the transfer of electrons to and from the cytochrome molecule.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
11742117 S.Geremia, G.Garau, L.Vaccari, R.Sgarra, M.S.Viezzoli, M.Calligaris, and L.Randaccio (2002).
Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.
  Protein Sci, 11, 6.
PDB codes: 1fj0 1i8o 1i8p
  9385633 A.C.Wallace, N.Borkakoti, and J.M.Thornton (1997).
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
  Protein Sci, 6, 2308-2323.  
  8976558 M.Ubbink, M.Pfuhl, J.van der Oost, A.Berg, and G.W.Canters (1996).
NMR assignments and relaxation studies of Thiobacillus versutus ferrocytochrome c-550 indicate the presence of a highly mobile 13-residues long C-terminal tail.
  Protein Sci, 5, 2494-2505.  
7583671 P.A.Williams, V.Fülöp, Y.C.Leung, C.Chan, J.W.Moir, G.Howlett, S.J.Ferguson, S.E.Radford, and J.Hajdu (1995).
Pseudospecific docking surfaces on electron transfer proteins as illustrated by pseudoazurin, cytochrome c550 and cytochrome cd1 nitrite reductase.
  Nat Struct Biol, 2, 975-982.
PDB code: 1adw
7508392 B.Samyn, B.C.Berks, M.D.Page, S.J.Ferguson, and J.J.van Beeumen (1994).
Characterisation and amino acid sequence of cytochrome c-550 from Thiosphaera pantotropha.
  Eur J Biochem, 219, 585-594.  
8168550 M.Caffrey, B.Brutscher, J.P.Simorre, J.Fitch, M.Cusanovich, and D.Marion (1994).
Assignment of the 13C and 13CO resonances for Rhodobacter capsulatus ferrocytochrome c2 using double-resonance and triple-resonance NMR spectroscopy.
  Eur J Biochem, 221, 63-75.  
8020493 M.Ubbink, N.I.Hunt, H.A.Hill, and G.W.Canters (1994).
Kinetics of the reduction of wild-type and mutant cytochrome c-550 by methylamine dehydrogenase and amicyanin from Thiobacillus versutus.
  Eur J Biochem, 222, 561-571.  
1907667 J.Rose, and F.Eisenmenger (1991).
A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm.
  J Mol Evol, 32, 340-354.  
2107323 M.S.Johnson, M.J.Sutcliffe, and T.L.Blundell (1990).
Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins.
  J Mol Evol, 30, 43-59.  
  2153663 R.J.Van Spanning, C.Wansell, N.Harms, L.F.Oltmann, and A.H.Stouthamer (1990).
Mutagenesis of the gene encoding cytochrome c550 of Paracoccus denitrificans and analysis of the resultant physiological effects.
  J Bacteriol, 172, 986-996.  
2560195 J.S.Fetrow, T.S.Cardillo, and F.Sherman (1989).
Deletions and replacements of omega loops in yeast iso-1-cytochrome c.
  Proteins, 6, 372-381.  
  2991202 M.Husain, and D.J.Steenkamp (1985).
Partial purification and characterization of glutaryl-coenzyme A dehydrogenase, electron transfer flavoprotein, and electron transfer flavoprotein-Q oxidoreductase from Paracoccus denitrificans.
  J Bacteriol, 163, 709-715.  
6667333 W.Kabsch, and C.Sander (1983).
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
  Biopolymers, 22, 2577-2637.  
6285999 J.P.Allen, J.T.Colvin, D.G.Stinson, C.P.Flynn, and H.J.Stapleton (1982).
Protein conformation from electron spin relaxation data.
  Biophys J, 38, 299-310.  
6267311 M.L.Baba, L.L.Darga, M.Goodman, and J.Czelusniak (1981).
Evolution of cytochrome C investigated by the maximum parsimony method.
  J Mol Evol, 17, 197-213.  
6243179 R.E.Dickerson (1980).
Evolution and gene transfer in purple photosynthetic bacteria.
  Nature, 283, 210-212.  
203462 D.J.Cookson, G.R.Moore, R.C.Pitt, R.J.Williams, I.D.Campbell, R.P.Ambler, M.Bruschi, and J.LeGall (1978).
Structural homology of cytochromes c.
  Eur J Biochem, 83, 261-275.  
96440 R.J.Almassy, and R.E.Dickerson (1978).
Pseudomonas cytochrome c551 at 2.0 A resolution: enlargement of the cytochrome c family.
  Proc Natl Acad Sci U S A, 75, 2674-2678.  
  353480 V.A.Saunders (1978).
Genetics of Rhodospirillaceae.
  Microbiol Rev, 42, 357-384.  
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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