PDBsum entry 5cib

Electron transport/oxidoreductase

PDB id: 5cib

Contents

Protein chains

294 a.a.

108 a.a.

Ligands

HEC ×4

51S ×2

PDB id:

5cib

Name:

Electron transport/oxidoreductase

Title:

Complex of yeast cytochromE C peroxidase (w191g) bound to 2,4- dimethylaniline with iso-1 cytochromE C

Structure:

CytochromE C peroxidase, mitochondrial. Chain: a, c. Fragment: cytochromE C peroxidase. Synonym: ccp. Engineered: yes. Mutation: yes. CytochromE C iso-1. Chain: b, d. Fragment: iso-1 cytochromE C.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: ccp1, ccp, cpo, ykr066c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: cyc1, yjr048w, j1653.

Resolution:

3.01Å R-factor: 0.242 R-free: 0.304

Authors:

B.R.Crane,T.M.Payne

Key ref:

T.M.Payne et al. (2016). Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c. Biochemistry, 55, 4807-4822. PubMed id: 27499202 DOI: 10.1021/acs.biochem.6b00262

Date:

11-Jul-15 Release date: 03-Aug-16

Protein chains

P00431  (CCPR_YEAST) -  Cytochrome c peroxidase, mitochondrial from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 361 a.a.

Struc: 294 a.a.*

Protein chains

P00044  (CYC1_YEAST) -  Cytochrome c isoform 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 109 a.a.

Struc: 108 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.1.11.1.5 - cytochrome-c peroxidase.
• Reaction: 2 Fe(II)-[cytochrome c] + H2O2 + 2 H⁺ = 2 Fe(III)-[cytochrome c] + 2 H2O
• Cofactor: Heme

Heme (Bound ligand (Het Group name = HEC) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1021/acs.biochem.6b00262

Biochemistry 55:4807-4822 (2016)

PubMed id: 27499202

Constraints on the Radical Cation Center of Cytochrome c Peroxidase for Electron Transfer from Cytochrome c.

T.M.Payne, E.F.Yee, B.Dzikovski, B.R.Crane.

ABSTRACT

The tryptophan 191 cation radical of cytochrome c peroxidase (CcP) compound I (Cpd I) mediates long-range electron transfer (ET) to cytochrome c (Cc). Here we test the effects of chemical substitution at position 191. CcP W191Y forms a stable tyrosyl radical upon reaction with peroxide and produces spectral properties similar to those of Cpd I but has low reactivity toward reduced Cc. CcP W191G and W191F variants also have low activity, as do redox ligands that bind within the W191G cavity. Crystal structures of complexes between Cc and CcP W191X (X = Y, F, or G), as well as W191G with four bound ligands reveal similar 1:1 association modes and heme pocket conformations. The ligands display structural disorder in the pocket and do not hydrogen bond to Asp235, as does Trp191. Well-ordered Tyr191 directs its hydroxyl group toward the porphyrin ring, with no basic residue in the range of interaction. CcP W191X (X = Y, F, or G) variants substituted with zinc-porphyrin (ZnP) undergo photoinduced ET with Cc(III). Their slow charge recombination kinetics that result from loss of the radical center allow resolution of difference spectra for the charge-separated state [ZnP(+), Cc(II)]. The change from a phenyl moiety at position 191 in W191F to a water-filled cavity in W191G produces effects on ET rates much weaker than the effects of the change from Trp to Phe. Low net reactivity of W191Y toward Cc(II) derives either from the inability of ZnP(+) or the Fe-CcP ferryl to oxidize Tyr or from the low potential of the resulting neutral Tyr radical.