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PDBsum entry 1kxn

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Oxidoreductase PDB id
1kxn
Jmol
Contents
Protein chain
289 a.a. *
Ligands
HEM
Waters ×348
* Residue conservation analysis
PDB id:
1kxn
Name: Oxidoreductase
Title: Crystal structure of cytochromE C peroxidase with a proposed electron transfer pathway excised to form a ligand binding channel.
Structure: CytochromE C peroxidase. Chain: a. Fragment: residues 72-362, numbered 4-292. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ccp-mkt. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.187     R-free:   0.194
Authors: R.J.Rosenfeld,A.M.A.Hayes,R.A.Musah,D.B.Goodin
Key ref:
R.J.Rosenfeld et al. (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. PubMed id: 11967381 DOI: 10.1110/ps.4870102
Date:
01-Feb-02     Release date:   06-Mar-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial
Seq:
Struc:
361 a.a.
289 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: 10.1110/ps.4870102 Protein Sci 11:1251-1259 (2002)
PubMed id: 11967381  
 
 
Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel.
R.J.Rosenfeld, A.M.Hays, R.A.Musah, D.B.Goodin.
 
  ABSTRACT  
 
A previously proposed electron transfer (ET) pathway in the heme enzyme cytochrome c peroxidase has been excised from the structure, leaving an open ligand-binding channel in its place. Earlier studies on cavity mutants of this enzyme have revealed structural plasticity in this region of the molecule. Analysis of these structures has allowed the design of a variant in which the specific section of protein backbone representing a previously proposed ET pathway is accurately extracted from the protein. A crystal structure verified the creation of an open channel that overlays the removed segment, extending from the surface of the protein to the heme at the core of the protein. A number of heterocyclic cations were found to bind to the proximal-channel mutant with affinities that can be rationalized based on the structures. It is proposed that small ligands bind more weakly to the proximal-channel mutant than to the W191G cavity due to an increased off rate of the open channel, whereas larger ligands are able to bind to the channel mutant without inducing large conformational changes. The structure of benzimidazole bound to the proximal-channel mutant shows that the ligand accurately overlays the position of the tryptophan radical center that was removed from the wild-type enzyme and displaces four of the eight ordered solvent molecules seen in the empty cavity. Ligand binding also caused a small rearrangement of the redesigned protein loop, perhaps as a result of improved electrostatic interactions with the ligand. The engineered channel offers the potential for introducing synthetic replacements for the removed structure, such as sensitizer-linked substrates. These installed "molecular wires" could be used to rapidly initiate reactions, trap reactive intermediates, or answer unresolved questions about ET pathways.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo views of the structures illustrating the design of the proximal-channel mutant. The views in A and B are rotated by 90. In blue is the structure of the W191G mutant in the closed conformation, in which the electron transfer pathway residues are in the same conformation as the wild-type enzyme. Shown in green is the structure of the same mutant in the open conformation with benzimidazole bound. The cis-trans isomerization of Pro 190 and the main-chain-side-chain interchange of Asn 195 serve as the hinge points for the conformational switch. Shown in white is the structure of the channel mutant in the absence of ligand.
Figure 4.
Fig. 4. Solvent-excluded surface representation of the engineered proximal-channel mutant in its ligand-free (A) and benzimidazole-bound forms (B). For both A and B, the surface was calculated using a 1.5- radius probe sphere using the MSMS program. Clipping planes are used to generate a thin slice of the engineered channel in which the front surface of the invaginated channel is removed. The heme is shown in red and the ribbon representation of the protein is shown in brown. In A, the proposed electron transfer pathway and Trp 191 radical site from wild-type cytochrome c peroxidase is shown superimposed on this channel in blue. In B, the F[o]-F[c] omit electron density is shown at 7 (blue) for a crystal soaked in benzimidazole, in which no model for the ligand was included for several refinement cycles. The refined position of benzimidazole is also shown in yellow.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2002, 11, 1251-1259) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19072042 A.M.Hays Putnam, Y.T.Lee, and D.B.Goodin (2009).
Replacement of an electron transfer pathway in cytochrome c peroxidase with a surrogate peptide.
  Biochemistry, 48, 1-3.
PDB code: 3exb
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.  
12487424 R.B.van Huystee, Y.Sun, and B.Lige (2002).
A retrospective look at the cationic peanut peroxidase structure.
  Crit Rev Biotechnol, 22, 335-354.  
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.