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PDBsum entry 1dsp

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protein ligands links
Oxidoreductase PDB id
1dsp
Jmol
Contents
Protein chain
291 a.a. *
Ligands
HEM-IMD
Waters ×129
* Residue conservation analysis
PDB id:
1dsp
Name: Oxidoreductase
Title: CytochromE C peroxidase h175g mutant, imidazole complex at ph 7, room temperature.
Structure: CytochromE C peroxidase. Chain: a. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.03Å     R-factor:   0.206    
Authors: J.Hirst,S.K.Wilcox,P.A.Williams,D.E.Mcree,D.B.Goodin
Key ref:
J.Hirst et al. (2001). Replacement of the axial histidine ligand with imidazole in cytochrome c peroxidase. 1. Effects on structure. Biochemistry, 40, 1265-1273. PubMed id: 11170452 DOI: 10.1021/bi002089r
Date:
07-Jan-00     Release date:   07-Mar-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial
Seq:
Struc:
361 a.a.
291 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.11.1.5  - Cytochrome-c peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 ferrocytochrome c + H2O2 = 2 ferricytochrome c + 2 H2O
2 × ferrocytochrome c
+ H(2)O(2)
= 2 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     peroxidase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi002089r Biochemistry 40:1265-1273 (2001)
PubMed id: 11170452  
 
 
Replacement of the axial histidine ligand with imidazole in cytochrome c peroxidase. 1. Effects on structure.
J.Hirst, S.K.Wilcox, P.A.Williams, J.Blankenship, D.E.McRee, D.B.Goodin.
 
  ABSTRACT  
 
Replacement of the axial histidine ligand with exogenous imidazole has been accomplished in a number of heme protein mutants, where it often serves to complement the functional properties of the protein. In this paper, we describe the effects of pH and buffer ion on the crystal structure of the H175G mutant of cytochrome c peroxidase, in which the histidine tether between the heme and the protein backbone is replaced by bound imidazole. The structures show that imidazole can occupy the proximal H175G cavity under a number of experimental conditions, but that the details of the interaction with the protein and the coordination to the heme are markedly dependent on conditions. Replacement of the tethered histidine ligand with imidazole permits the heme to shift slightly in its pocket, allowing it to adopt either a planar or distally domed conformation. H175G crystallized from both high phosphate and imidazole concentrations exists as a novel, 5-coordinate phosphate bound state, in which the proximal imidazole is dissociated and the distal phosphate is coordinated to the iron. To accommodate this bound phosphate, the side chains of His-52 and Asn-82 alter their positions and a significant conformational change in the surrounding protein backbone occurs. In the absence of phosphate, imidazole binds to the proximal H175G cavity in a pH-dependent fashion. At pH 7, imidazole is directly coordinated to the heme (d(Fe--Im) = 2.0 A) with a nearby distal water (d(Fe--HOH) = 2.4 A). This is similar to the structure of WT CCP except that the iron lies closer in the heme plane, and the hydrogen bond between imidazole and Asp-235 (d(Im--Asp) = 3.1 A) is longer than for WT CCP (d(His--Asp) = 2.9 A). As the pH is dropped to 5, imidazole dissociates from the heme (d(Fe--Im) = 2.9 A), but remains in the proximal cavity where it is strongly hydrogen bonded to Asp-235 (d(Im--Asp) = 2.8 A). In addition, the heme is significantly domed toward the distal pocket where it may coordinate a water molecule. Finally, the structure of H175G/Im, pH 6, at low temperature (100 K) is very similar to that at room temperature, except that the water above the distal heme face is not present. This study concludes that steric restrictions imposed by the covalently tethered histidine restrain the heme and its ligand coordination from distortions that would arise in the absence of the restricted tether. Coupled with the functional and spectroscopic properties described in the following paper in this issue, these structures help to illustrate how the delicate and critical interactions between protein, ligand, and metal modulate the function of heme enzymes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18923851 S.W.Vetter, A.C.Terentis, R.L.Osborne, J.H.Dawson, and D.B.Goodin (2009).
Replacement of the axial histidine heme ligand with cysteine in nitrophorin 1: spectroscopic and crystallographic characterization.
  J Biol Inorg Chem, 14, 179-191.  
17009275 K.Kobayashi, M.Kubo, S.Yoshioka, T.Kitagawa, Y.Kato, Y.Asano, and S.Aono (2006).
Systematic regulation of the enzymatic activity of phenylacetaldoxime dehydratase by exogenous ligands.
  Chembiochem, 7, 2004-2009.  
12538891 A.M.Hays, H.B.Gray, and D.B.Goodin (2003).
Trapping of peptide-based surrogates in an artificially created channel of cytochrome c peroxidase.
  Protein Sci, 12, 278-287.  
11967381 R.J.Rosenfeld, A.M.Hays, R.A.Musah, and D.B.Goodin (2002).
Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel.
  Protein Sci, 11, 1251-1259.
PDB codes: 1kxm 1kxn
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.