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PDBsum entry 2bc5
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protein ligands Protein-protein interface(s) links
Electron transport PDB id
2bc5

 

 

 

 

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Contents
Protein chains
106 a.a. *
Ligands
SO4 ×9
HEC ×4
Waters ×132
* Residue conservation analysis
PDB id:
2bc5
Name: Electron transport
Title: Crystal structure of e. Coli cytochrome b562 with engineered c-type heme linkages
Structure: Soluble cytochrome b562. Chain: a, b, c, d. Synonym: cytochrome b-562. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.25Å     R-factor:   0.239     R-free:   0.277
Authors: J.Faraone-Mennella,F.A.Tezcan,H.B.Gray,J.R.Winkler
Key ref:
J.Faraone-Mennella et al. (2006). Stability and folding kinetics of structurally characterized cytochrome c-b562. Biochemistry, 45, 10504-10511. PubMed id: 16939202 DOI: 10.1021/bi060242x
Date:
18-Oct-05     Release date:   26-Sep-06    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ABE7  (C562_ECOLX) -  Soluble cytochrome b562 from Escherichia coli
Seq:
Struc: 		128 a.a.
106 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1021/bi060242x Biochemistry 45:10504-10511 (2006)
PubMed id: 16939202  
 
 
Stability and folding kinetics of structurally characterized cytochrome c-b562.
J.Faraone-Mennella, F.A.Tezcan, H.B.Gray, J.R.Winkler.
 
  ABSTRACT  
 
The four-helix-bundle protein fold can be constructed from a wide variety of primary amino acid sequences. Proteins with this structure are excellent candidates for investigations of the relationship between folding mechanism and topology. The folding of cytochrome b(562), a four-helix-bundle heme protein, is hampered by heme dissociation. To overcome this complication, we have engineered a variant of cytochrome b(562) (cyt c-b(562)) featuring a c-type linkage between the heme and the polypeptide chain. The replacement of the native cyt b(562) leader sequence in this protein with that of a c-type cytochrome (cyt c(556)) led to high yields of fully matured and correctly folded cyt c-b(562). We have determined the X-ray crystal structure of cyt c-b(562) at 2.25 A and characterized its physical, chemical, and folding properties. These measurements reveal that the c-type linkage does not perturb the protein fold or reduction potential of the heme group. The covalent attachment of the porphyrin to the polypeptide does, however, produce a substantial change in protein stability and folding kinetics.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20192262 E.N.Salgado, R.J.Radford, and F.A.Tezcan (2010).
Metal-directed protein self-assembly.
  Acc Chem Res, 43, 661-672.  
20080561 E.N.Salgado, X.I.Ambroggio, J.D.Brodin, R.A.Lewis, B.Kuhlman, and F.A.Tezcan (2010).
Metal templated design of protein interfaces.
  Proc Natl Acad Sci U S A, 107, 1827-1832.
PDB codes: 3hni 3hnj 3hnk 3hnl
20377257 R.J.Radford, P.C.Nguyen, T.B.Ditri, J.S.Figueroa, and F.A.Tezcan (2010).
Controlled protein dimerization through hybrid coordination motifs.
  Inorg Chem, 49, 4362-4369.
PDB code: 3l1m
18636480 C.Negron, C.Fufezan, and R.L.Koder (2009).
Geometric constraints for porphyrin binding in helical protein binding sites.
  Proteins, 74, 400-416.  
19416896 T.Kimura, J.C.Lee, H.B.Gray, and J.R.Winkler (2009).
Folding energy landscape of cytochrome cb562.
  Proc Natl Acad Sci U S A, 106, 7834-7839.  
17933771 C.J.Reedy, M.M.Elvekrog, and B.R.Gibney (2008).
Development of a heme protein structure-electrochemical function database.
  Nucleic Acids Res, 36, D307-D313.  
18422313 E.N.Salgado, R.A.Lewis, J.Faraone-Mennella, and F.A.Tezcan (2008).
Metal-mediated self-assembly of protein superstructures: influence of secondary interactions on protein oligomerization and aggregation.
  J Am Chem Soc, 130, 6082-6084.
PDB codes: 3c62 3c63
17616605 T.Gao, and M.R.O'Brian (2007).
Control of DegP-dependent degradation of c-type cytochromes by heme and the cytochrome c maturation system in Escherichia coli.
  J Bacteriol, 189, 6253-6259.  
17179212 T.Kimura, J.C.Lee, H.B.Gray, and J.R.Winkler (2007).
Site-specific collapse dynamics guide the formation of the cytochrome c' four-helix bundle.
  Proc Natl Acad Sci U S A, 104, 117-122.  
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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