PDBsum entry 1zzh

Oxidoreductase

PDB id: 1zzh

Contents

Protein chains

297 a.a. *

Ligands

HEC ×8

Metals

_CA ×4

_ZN ×8

Waters ×36

* Residue conservation analysis

PDB id:

1zzh

Name:

Oxidoreductase

Title:

Structure of the fully oxidized di-heme cytochromE C peroxidase from r. Capsulatus

Structure:

CytochromE C peroxidase. Chain: a, b, c, d. Engineered: yes

Source:

Rhodobacter capsulatus. Organism_taxid: 1061. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Tetramer (from PQS)

Resolution:

2.70Å R-factor: 0.249 R-free: 0.278

Authors:

L.De Smet,S.N.Savvides,E.Van Horen,G.Pettigrew,J.J.Van Beeumen

Key ref:

L.De Smet et al. (2006). Structural and mutagenesis studies on the cytochrome c peroxidase from Rhodobacter capsulatus provide new insights into structure-function relationships of bacterial di-heme peroxidases. J Biol Chem, 281, 4371-4379. PubMed id: 16314410 DOI: 10.1074/jbc.M509582200

Date:

14-Jun-05 Release date: 29-Nov-05

Protein chains

No UniProt id for this chain

Struc: 297 a.a.

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 = HEC) matches with 95.45% similarity)

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

Added reference

DOI no: 10.1074/jbc.M509582200

J Biol Chem 281:4371-4379 (2006)

PubMed id: 16314410

Structural and mutagenesis studies on the cytochrome c peroxidase from Rhodobacter capsulatus provide new insights into structure-function relationships of bacterial di-heme peroxidases.

L.De Smet, S.N.Savvides, E.Van Horen, G.Pettigrew, J.J.Van Beeumen.

ABSTRACT

Cytochrome c peroxidases (CCP) play a key role in cellular detoxification by catalyzing the reduction of hydrogen peroxide to water. The di-heme CCP from Rhodobacter capsulatus is the fastest enzyme (1060 s(-1)), when tested with its physiological cytochrome c substrate, among all di-heme CCPs characterized to date and has, therefore, been an attractive target to investigate structure-function relationships for this family of enzymes. Here, we combine for the first time structural studies with site-directed mutagenesis and spectroscopic studies of the mutant enzymes to investigate the roles of amino acid residues that have previously been suggested to be important for activity. The crystal structure of R. capsulatus at 2.7 Angstroms in the fully oxidized state confirms the overall molecular scaffold seen in other di-heme CCPs but further reveals that a segment of about 10 amino acids near the peroxide binding site is disordered in all four molecules in the asymmetric unit of the crystal. Structural and sequence comparisons with other structurally characterized CCPs suggest that flexibility in this part of the molecular scaffold is an inherent molecular property of the R. capsulatus CCP and of CCPs in general and that it correlates with the levels of activity seen in CCPs characterized, thus, far. Mutagenesis studies support the spin switch model and the roles that Met-118, Glu-117, and Trp-97 play in this model. Our results help to clarify a number of aspects of the debate on structure-function relationships in this family of bacterial CCPs and set the stage for future studies.

Selected figure(s)

Figure 1.
Structure of RcCCP and comparisons with other CCPs. A, stereo view of the overall structure and location of the mutated residues as is discussed under “Results and Discussion.” B, details of the calcium binding site. wat, water. C, stereo view of a structural superposition of RcCCP (green) with PaCCP (red, PDB code 1EB7) and PnCCP-IN (blue, PDB code 1RZ6). D, close-up view of the flexible structural segments in the region of the low potential heme.

Figure 7.
Positioning of the heme groups relative to the proposed electron relay residue Trp-97.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 4371-4379) copyright 2006.

Figures were selected by an automated process.