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PDBsum entry 3cyt
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protein ligands Protein-protein interface(s) links
Electron transport (heme protein) PDB id
3cyt

 

 

 

 

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Contents
Protein chains
104 a.a. *
Ligands
HEC ×2
Waters ×51
* Residue conservation analysis
PDB id:
3cyt
Name: Electron transport (heme protein)
Title: Redox conformation changes in refined tuna cytochromE C
Structure: CytochromE C. Chain: o, i. Engineered: yes
Source: Thunnus alalunga. Albacore. Organism_taxid: 8235
Resolution:
1.80Å     R-factor:   not given    
Authors: T.Takano
Key ref: T.Takano and R.E.Dickerson (1980). Redox conformation changes in refined tuna cytochrome c. Proc Natl Acad Sci U S A, 77, 6371-6375. PubMed id: 6256733 DOI: 10.1073/pnas.77.11.6371
Date:
01-Jul-80     Release date:   16-Sep-80    
Supersedes: 1cyt
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P81459  (CYC_THUAA) -  Cytochrome c from Thunnus alalunga
Seq:
Struc: 		103 a.a.
103 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.77.11.6371 Proc Natl Acad Sci U S A 77:6371-6375 (1980)
PubMed id: 6256733  
 
 
Redox conformation changes in refined tuna cytochrome c.
T.Takano, R.E.Dickerson.
 
  ABSTRACT  
 
Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer to the heme and the heme has moved 0.15 A out of its heme crevice; both changes lead to a more polar microenvironment for the heme. Chemical modification studies, patterns of evolutionary conservatism, structural differences in bacterial cytochromes, and x-ray studies all agree that the "active site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87 (thus containing the evolutionary conservative 72-87 loop) and has the buried water molecule just below its surface and the opening of the heme crevice slightly to one side.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17142287 L.Giachini, F.Francia, L.Cordone, F.Boscherini, and G.Venturoli (2007).
Cytochrome C in a dry trehalose matrix: structural and dynamical effects probed by x-ray absorption spectroscopy.
  Biophys J, 92, 1350-1360.  
16383355 J.Y.Chen, J.R.Knab, J.Cerne, and A.G.Markelz (2005).
Large oxidation dependence observed in terahertz dielectric response for cytochrome c.
  Phys Rev E Stat Nonlin Soft Matter Phys, 72, 040901.  
12084923 F.A.Tezcan, W.M.Findley, B.R.Crane, S.A.Ross, J.G.Lyubovitsky, H.B.Gray, and J.R.Winkler (2002).
Using deeply trapped intermediates to map the cytochrome c folding landscape.
  Proc Natl Acad Sci U S A, 99, 8626-8630.
PDB code: 1lfm
11939594 O.V.Tsodikov, M.T.Record, and Y.V.Sergeev (2002).
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
  J Comput Chem, 23, 600-609.  
12011418 T.Simonson (2002).
Gaussian fluctuations and linear response in an electron transfer protein.
  Proc Natl Acad Sci U S A, 99, 6544-6549.  
11679712 A.Camara-Artigas, J.C.Williams, and J.P.Allen (2001).
Structure of cytochrome c2 from Rhodospirillum centenum.
  Acta Crystallogr D Biol Crystallogr, 57, 1498-1505.
PDB code: 1jdl
11296248 F.A.Tezcan, B.R.Crane, J.R.Winkler, and H.B.Gray (2001).
Electron tunneling in protein crystals.
  Proc Natl Acad Sci U S A, 98, 5002-5006.
PDB codes: 1i54 1i55
11248126 H.Hanzawa, K.Inomata, H.Kinoshita, T.Kakiuchi, K.P.Jayasundera, D.Sawamoto, A.Ohta, K.Uchida, K.Wada, and M.Furuya (2001).
In vitro assembly of phytochrome B apoprotein with synthetic analogs of the phytochrome chromophore.
  Proc Natl Acad Sci U S A, 98, 3612-3617.  
11133964 M.Santana, M.M.Pereira, N.P.Elias, C.M.Soares, and M.Teixeira (2001).
Gene cluster of Rhodothermus marinus high-potential iron-sulfur Protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases.
  J Bacteriol, 183, 687-699.  
9636061 A.K.Bhuyan, and J.B.Udgaonkar (1998).
Multiple kinetic intermediates accumulate during the unfolding of horse cytochrome c in the oxidized state.
  Biochemistry, 37, 9147-9155.  
9485396 J.S.Fetrow, J.S.Spitzer, B.M.Gilden, S.J.Mellender, T.J.Begley, B.J.Haas, and T.L.Boose (1998).
Structure, function, and temperature sensitivity of directed, random mutants at proline 76 and glycine 77 in omega-loop D of yeast iso-1-cytochrome c.
  Biochemistry, 37, 2477-2487.  
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.  
9062118 K.Qu, J.L.Vaughn, A.Sienkiewicz, C.P.Scholes, and J.S.Fetrow (1997).
Kinetics and motional dynamics of spin-labeled yeast iso-1-cytochrome c: 1. Stopped-flow electron paramagnetic resonance as a probe for protein folding/unfolding of the C-terminal helix spin-labeled at cysteine 102.
  Biochemistry, 36, 2884-2897.  
  9194181 M.H.Zehfus (1997).
Identification of compact, hydrophobically stabilized domains and modules containing multiple peptide chains.
  Protein Sci, 6, 1210-1219.  
  7549883 M.H.Zehfus (1995).
Automatic recognition of hydrophobic clusters and their correlation with protein folding units.
  Protein Sci, 4, 1188-1202.  
7567963 R.B.Yelle, N.S.Park, and T.Ichiye (1995).
Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: changes in structure and electrostatic potential during redox reactions.
  Proteins, 22, 154-167.  
  8563637 R.M.Stroud, and E.B.Fauman (1995).
Significance of structural changes in proteins: expected errors in refined protein structures.
  Protein Sci, 4, 2392-2404.  
7805627 R.W.Woody (1994).
Contributions of tryptophan side chains to the far-ultraviolet circular dichroism of proteins.
  Eur Biophys J, 23, 253-262.  
8033888 Y.Huang, S.Beeser, J.G.Guillemette, R.K.Storms, and J.A.Kornblatt (1994).
Mutations of iso-1-cytochrome c at positions 13 and 90. Separate effects on physical and functional properties.
  Eur J Biochem, 223, 155-160.  
8394001 M.H.Zehfus (1993).
Improved calculations of compactness and a reevaluation of continuous compact units.
  Proteins, 16, 293-300.  
  8390883 Z.Zhang, and D.L.Smith (1993).
Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation.
  Protein Sci, 2, 522-531.  
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.  
1646659 T.Simonson, D.Perahia, and A.T.Brünger (1991).
Microscopic theory of the dielectric properties of proteins.
  Biophys J, 59, 670-690.  
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.  
2848101 S.H.Northrup, J.A.Luton, J.O.Boles, and J.C.Reynolds (1988).
Brownian dynamics simulation of protein association.
  J Comput Aided Mol Des, 1, 291-311.  
3017716 J.A.Kornblatt, A.M.English, and G.Hui Bon Hoa (1986).
The effects of pressure on yeast cytochrome c peroxidase.
  Eur J Biochem, 159, 39-43.  
2867101 K.Schwerzmann, L.M.Cruz-Orive, R.Eggman, A.Sänger, and E.R.Weibel (1986).
Molecular architecture of the inner membrane of mitochondria from rat liver: a combined biochemical and stereological study.
  J Cell Biol, 102, 97.  
6378653 J.L.Dreyer (1984).
Electron transfer in biological systems: an overview.
  Experientia, 40, 653-675.  
16593405 R.F.Goldstein, and A.Bearden (1984).
Tunneling in Chromatium chromatophores: Detection of a Hopfield charge-transfer band.
  Proc Natl Acad Sci U S A, 81, 135-139.  
6091118 S.Rackovsky, and D.A.Goldstein (1984).
On the redox conformational change in cytochrome c.
  Proc Natl Acad Sci U S A, 81, 5901-5905.  
6305654 M.Duñach, M.Sabés, and E.Padrós (1983).
Fourth-derivative spectrophotometry analysis of tryptophan environment in proteins. Application to melittin, cytochrome c and bacteriorhodopsin.
  Eur J Biochem, 134, 123-128.  
6278497 D.Eden, J.B.Matthew, J.J.Rosa, and F.M.Richards (1982).
Increase in apparent compressibility of cytochrome c upon oxidation.
  Proc Natl Acad Sci U S A, 79, 815-819.  
6274637 P.Rosen, M.Segal, and I.Pecht (1981).
Electron transfer between azurin from Alcaligenes faecalis and cytochrome c551 from Pseudomonas aeruginosa.
  Eur J Biochem, 120, 339-344.  
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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