PDBsum entry 1eb7

Oxidoreductase

PDB id: 1eb7

Contents

Protein chain

317 a.a. *

Ligands

HEC ×2

Metals

_CA

Waters ×73

* Residue conservation analysis

PDB id:

1eb7

Name:

Oxidoreductase

Title:

Crystal structure of the di-haem cytochromE C peroxidase from pseudomonas aeruginosa

Structure:

Cytochrome c551 peroxidase. Chain: a. Synonym: cytochromE C peroxidase, ccp, di-haem cytochromE C peroxidase. Ec: 1.11.1.5

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Strain: ntcc 6750

Biol. unit:

Dimer (from PDB file)

Resolution:

2.40Å R-factor: 0.172 R-free: 0.220

Authors:

V.Fulop

Key ref:

V.Fülöp et al. (1995). Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa. Structure, 3, 1225-1233. PubMed id: 8591033 DOI: 10.1016/S0969-2126(01)00258-1

Date:

24-Jul-01 Release date: 24-Jul-01

Protein chain

P14532  (CCPR_PSEAE) -  Cytochrome c551 peroxidase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 346 a.a.

Struc: 317 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: 10.1016/S0969-2126(01)00258-1

Structure 3:1225-1233 (1995)

PubMed id: 8591033

Crystal structure of the di-haem cytochrome c peroxidase from Pseudomonas aeruginosa.

V.Fülöp, C.J.Ridout, C.Greenwood, J.Hajdu.

ABSTRACT

BACKGROUND: Cytochrome c peroxidase from Pseudomonas aeruginosa (PsCCP) represents a new class of peroxidases which work without the need to create a semi-stable free radical for catalysis. The enzyme is located in the bacterial periplasm where its likely function is to provide protection against toxic peroxides. The soluble 323-residue single polypeptide chain contains two covalent c-type haems with very different properties: one of them is a low-potential (-330 mV) centre where hydrogen peroxide is reduced (the peroxidatic site); the other is a high-potential (+320 mV) centre which feeds electrons to the peroxidatic site from soluble electron-shuttle proteins such as cytochrome c and azurin. RESULTS: The crystal structure of the oxidized form of PsCCP has been determined to 2.4 A resolution by multiple isomorphous replacement, and refined to an R-factor of 19.2%. PsCCP is organized into two domains, both of them containing a covalent c-haem in a structure reminiscent of class 1 cytochromes c. The domains are related by a quasi-twofold axis. The domain interface holds a newly discovered calcium-binding site with an unusual set of ligands. CONCLUSIONS: The likely function of the calcium site is to maintain the structural integrity of the enzyme and/or to modulate electron transfer between the two haem domains. The low-potential haem has two histidine axial ligands (His55 and His71) and the high-potential haem is ligated by His201 and Met275. There are no polar residues at the peroxidatic site in the inactive oxidized enzyme. The structure suggests that, in the half-reduced functional form of the enzyme, the low-potential haem has to shed His71 in order to make the enzyme catalytically competent. This process is likely to trigger a reorganization of the active site, and may introduce a new residues into the haem pocket.

Selected figure(s)

Figure 3.
Figure 3. The structure of cytochrome c peroxidase from P. aeruginosa. The ribbon diagram is colour-ramped blue to red from the N to the C terminus. The small grey sphere shows the location of the calcium ion and the haems are in ball-and-stick representation. LP and HP denote low-potential and high-potential haem domains, respectively. Figure 3. The structure of cytochrome c peroxidase from P. aeruginosa. The ribbon diagram is colour-ramped blue to red from the N to the C terminus. The small grey sphere shows the location of the calcium ion and the haems are in ball-and-stick representation. LP and HP denote low-potential and high-potential haem domains, respectively.

Figure 5.
Figure 5. Comparison of the fold of the c-type cytochrome domains of PsCCP with the fold of typical class 1 cytochromes c. (a) High-potential haem domain of PsCCP. (b) Low-potential haem domain of PsCCP. (c) Cytochrome c[551] from P. aeruginosa (PDB [23] entry 351C). (d) Tuna cytochrome c (PDB entry 3CYT). The cytochromes are colour-ramped dark blue to light blue from the N to the C terminus. The PsCCP domains are coloured similarly. The haems are shown in ball-and-stick representation. Figure 5. Comparison of the fold of the c-type cytochrome domains of PsCCP with the fold of typical class 1 cytochromes c. (a) High-potential haem domain of PsCCP. (b) Low-potential haem domain of PsCCP. (c) Cytochrome c[551] from P. aeruginosa (PDB [[6]23] entry 351C). (d) Tuna cytochrome c (PDB entry 3CYT). The cytochromes are colour-ramped dark blue to light blue from the N to the C terminus. The PsCCP domains are coloured similarly. The haems are shown in ball-and-stick representation.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1225-1233) copyright 1995.

Figures were selected by an automated process.