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PDBsum entry 1csv

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Electron transport(heme protein) PDB id
1csv
Jmol
Contents
Protein chain
108 a.a. *
Ligands
SO4
HEM
Waters ×58
* Residue conservation analysis
PDB id:
1csv
Name: Electron transport(heme protein)
Title: Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochromE C
Structure: CytochromE C. Chain: a. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Resolution:
1.90Å     R-factor:   0.192    
Authors: T.P.Lo,G.D.Brayer
Key ref:
T.P.Lo et al. (1995). Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c. Protein Sci, 4, 198-208. PubMed id: 7757009 DOI: 10.1002/pro.5560040207
Date:
04-Oct-94     Release date:   26-Jan-95    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00044  (CYC1_YEAST) -  Cytochrome c iso-1
Seq:
Struc:
109 a.a.
108 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     respiratory chain   3 terms 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     electron carrier activity     5 terms  

 

 
DOI no: 10.1002/pro.5560040207 Protein Sci 4:198-208 (1995)
PubMed id: 7757009  
 
 
Replacements in a conserved leucine cluster in the hydrophobic heme pocket of cytochrome c.
T.P.Lo, M.E.Murphy, J.G.Guillemette, M.Smith, G.D.Brayer.
 
  ABSTRACT  
 
A cluster of highly conserved leucine side chains from residues 9, 68, 85, 94, and 98 is located in the hydrophobic heme pocket of cytochrome c. The contributions of two of these, Leu 85 and Leu 94, have been studied using a protein structure-function-mutagenesis approach to probe their roles in the maintenance of overall structural integrity and electron transfer activity. Structural studies of the L85C, L85F, L85M, and L94S mutant proteins show that, in each case, the overall fold of cytochrome c is retained, but that localized conformational shifts are required to accommodate the introduced side chains. In particular, the side chains of Cys 85 and Phe 85 form energetically favorable interactions with Phe 82, whereas Met 85 takes on a more remote conformation to prevent an unfavorable interaction with the phenyl ring of Phe 82. In the case of the L94S mutant protein, the new polar group introduced is found to form hydrogen bonds to nearby carbonyl groups. In all proteins with substitutions at Leu 85, the hydrophobic nature of the heme pocket is preserved and no significant decrease in heme reduction potential is observed. Despite earlier predictions that Leu 85 is an important determinant in cytochrome c electron transfer partner complexation, our studies show this is unlikely to be the case because the considerable surface contour perturbations made by substitutions at this residue do not correspondingly translate into significant changes in electron transfer rates. For the L94S mutant protein, the substitution of a polar hydroxyl group directly into the hydrophobic heme pocket has a larger effect on heme reduction potential, but this is mitigated by two factors. First, the side chain of Ser 94 is rotated away from the heme group and, second, the side chain of Leu 98 shifts into a portion of the new space available, partially shielding the heme group. The Leu 94 Ser substitution does not perturb the highly conserved interface formed by the nearly perpendicular packing of the N- and C-terminal helices of cytochrome c, ruling this out as the cause of this mutant protein becoming thermally labile and having a lower functional activity. Our results show these effects are most likely attributable to disruption of the heme pocket region. Much of the ability of cytochrome c to absorb the introduction of mutations at Leu 85 and Leu 94 appears to be a consequence of the conformational flexibility afforded by the leucine cluster in this region as well as the presence of a nearby internal cavity.(ABSTRACT TRUNCATED AT 400 WORDS)
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Stereo iagra showing the region about Leu 94 intheL94Smutant protein. Thestructure of thewild-typeproteinhasbeensuperimposed and is shown withthick lines, whereasthemutantprotein structureisdepicted by thin lines. Altered side-chain conformations for Leu 9 andLeu98areclearly evi- dent. Hydrogen bonds formedbetweenthehydroxyl group of Ser94andthe main-chain carbonyl oxygen atos of Asp 90 andArg91arerepresentedbydashed lines. Intrahelicalhydrogen bonds formedbetween thesecarbonyl groups and theamidenitrogen atoms of Leu 94 and Ile 95 are also epresntedbydashed lines.
Figure 5.
Fig. 5. Stereo diagram showing the location f thehydrophobicinternal cavity (dot surface) found in wild-type iso-1 cytochrome c. he heme group and nearby side chains that define the outer limits of this cavityin the L85F (thick lines) nd L94S (thin lines) mutant proteins havebeen superimposed onthe structure of te wild-type protein (medium lines). The differ- ent conformations observed for he Leu98 side chain are largely responsible for determining the size ofthis internal cavity. In the L85F mu- tant protein,the Leu 98 side chain moves into theinternal cavity, effectively eliminating this feature. In the L94S mutant protein, the Leu98 side chain moves toward the side chain of Ser 94, causing n increase in cavity size. The volume and surface area of this in a wide range of mutantprotins is tabulated in Table 5.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1995, 4, 198-208) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  10631980 J.R.Liggins, T.P.Lo, G.D.Brayer, and B.T.Nall (1999).
Thermal stability of hydrophobic heme pocket variants of oxidized cytochrome c.
  Protein Sci, 8, 2645-2654.  
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.  
  9007992 J.S.Fetrow, S.R.Horner, W.Oehrl, D.L.Schaak, T.L.Boose, and R.E.Burton (1997).
Analysis of the structure and stability of omega loop A replacements in yeast iso-1-cytochrome c.
  Protein Sci, 6, 197-210.  
8652519 S.F.Betz, J.L.Marmorino, A.J.Saunders, D.F.Doyle, G.B.Young, and G.J.Pielak (1996).
Unusual effects of an engineered disulfide on global and local protein stability.
  Biochemistry, 35, 7422-7428.  
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.