PDBsum entry 3m2d

Oxidoreductase

PDB id: 3m2d

Contents

Protein chain

291 a.a. *

Ligands

HEM

PO4

Waters ×630

* Residue conservation analysis

PDB id:

3m2d

Name:

Oxidoreductase

Title:

Crystallographic and single crystal spectral analysis of the peroxidase ferryl intermediate

Structure:

CytochromE C peroxidase, mitochondrial. Chain: a. Fragment: unp residues 71-361. Synonym: ccp. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 4932. Gene: ccp, ccp1, cpo, ykr066c. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.40Å R-factor: 0.117

Authors:

Y.T.Meharenna,T.L.Poulos

Key ref:

Y.T.Meharenna et al. (2010). Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate. Biochemistry, 49, 2984-2986. PubMed id: 20230048

Date:

06-Mar-10 Release date: 12-May-10

Protein chain

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

Seq: 361 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: 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 = HEM) matches with 95.45% similarity)

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

Added reference

Biochemistry 49:2984-2986 (2010)

PubMed id: 20230048

Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate.

Y.T.Meharenna, T.Doukov, H.Li, S.M.Soltis, T.L.Poulos.

ABSTRACT

The ferryl [Fe(IV)O] intermediate is important in many heme enzymes, and thus, the precise nature of the Fe(IV)-O bond is critical in understanding enzymatic mechanisms. The 1.40 A crystal structure of cytochrome c peroxidase Compound I has been determined as a function of X-ray dose while the visible spectrum was being monitored. The Fe-O bond increases in length from 1.73 A in the low-X-ray dose structure to 1.90 A in the high-dose structure. The low-dose structure correlates well with an Fe(IV) horizontal lineO bond, while we postulate that the high-dose structure is the cryo-trapped Fe(III)-OH species previously thought to be an Fe(IV)-OH species.