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PDBsum entry 1k3h

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protein ligands links
Electron transport PDB id
1k3h
Jmol
Contents
Protein chain
71 a.a. *
Ligands
HEC
* Residue conservation analysis
PDB id:
1k3h
Name: Electron transport
Title: Nmr solution structure of oxidized cytochromE C-553 from bacillus pasteurii
Structure: CytochromE C-553. Chain: a. Fragment: residues 22-92. Synonym: c553. Engineered: yes
Source: Sporosarcina pasteurii. Organism_taxid: 1474. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: L.Banci,I.Bertini,S.Ciurli,A.Dikiy,J.Dittmer,A.Rosato, G.Sciara,A.R.Thompsett
Key ref: L.Banci et al. (2002). NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria. Chembiochem, 3, 299-310. PubMed id: 11933230 DOI: 10.1002/1439-7633(20020402)3:4<299::AID-CBIC299>3.0.CO;2-0
Date:
03-Oct-01     Release date:   31-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P82599  (CY553_BACPA) -  Cytochrome c-553
Seq:
Struc:
92 a.a.
71 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     integral to membrane   1 term 
  Biochemical function     electron carrier activity     3 terms  

 

 
DOI no: 10.1002/1439-7633(20020402)3:4<299::AID-CBIC299>3.0.CO;2-0 Chembiochem 3:299-310 (2002)
PubMed id: 11933230  
 
 
NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
L.Banci, I.Bertini, S.Ciurli, A.Dikiy, J.Dittmer, A.Rosato, G.Sciara, A.R.Thompsett.
 
  ABSTRACT  
 
The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the available crystal structure. The solution structure is obtained from 1609 meaningful NOE data (22.7 per residue), 76 dihedral angles, and 59 pseudocontact shifts. The root mean square deviations from the average structure are 0.25+/-0.07 and 0.59+/-0.13 A for the backbone and all heavy atoms, respectively, and the quality assessment of the structure is satisfactory. The solution structure closely reproduces the fold observed in the crystal structure. The backbone mobility was then investigated through amide (15)N relaxation rate and (15)N-(1)H NOE measurements. The protein is rigid in both the sub-nanosecond and millisecond time scales, probably due to the relatively large heme:number of amino acids ratio. Modeling of eight c-type cytochromes from other Gram-positive bacteria with a high sequence identity (>30 %) to the present cytochrome c(553) was performed. Analysis of consensus features accounts for the relatively low reduction potential as being due to extensive heme hydration and indicates residues 34-35, 44-46, 69-72, and 75 as a conserved hydrophobic patch for the interaction with a protein partner. At variance with mitochondrial c-type cytochrome, this protein does not experience pH-dependent coordination equilibria. The reasons for this difference are analyzed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21359406 I.Bertini, G.Cavallaro, and A.Rosato (2011).
Principles and patterns in the interaction between mono-heme cytochrome c and its partners in electron transfer processes.
  Metallomics, 3, 354-362.  
21431228 M.K.Khan, H.Rahaman, and F.Ahmad (2011).
Conformation and thermodynamic stability of pre-molten and molten globule states of mammalian cytochromes-c.
  Metallomics, 3, 327-338.  
16292670 G.Kieseritzky, G.Morra, and E.W.Knapp (2006).
Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study.
  J Biol Inorg Chem, 11, 26-40.  
15691836 F.Musiani, A.Dikiy, A.Y.Semenov, and S.Ciurli (2005).
Structure of the intermolecular complex between plastocyanin and cytochrome f from spinach.
  J Biol Chem, 280, 18833-18841.
PDB code: 1ylb
16151864 I.Bertini, G.Cavallaro, and A.Rosato (2005).
A structural model for the adduct between cytochrome c and cytochrome c oxidase.
  J Biol Inorg Chem, 10, 613-624.
PDB code: 1zyy
15744766 J.A.Worrall, R.E.Diederix, M.Prudêncio, C.E.Lowe, S.Ciofi-Baffoni, M.Ubbink, and G.W.Canters (2005).
The effects of ligand exchange and mobility on the peroxidase activity of a bacterial cytochrome c upon unfolding.
  Chembiochem, 6, 747-758.  
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.