PDBsum entry 5sw4

Oxidoreductase

PDB id: 5sw4

Contents

Protein chains

713 a.a.

Ligands

HEM ×2

OXY

PO4 ×2

MPD ×3

TRS ×2

Metals

_NA ×2

Waters ×1553

PDB id:

5sw4

Name:

Oxidoreductase

Title:

Crystal structure of native catalase-peroxidase katg at ph8.0

Structure:

Catalase-peroxidase. Chain: a, b. Synonym: cp,peroxidase/catalase. Engineered: yes

Source:

Burkholderia pseudomallei (strain 1710b). Organism_taxid: 320372. Strain: 1710b. Gene: katg, burps1710b_3366. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.142 R-free: 0.171

Authors:

P.C.Loewen

Key ref:

X.Carpena et al. (2005). A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases. EMBO Rep, 6, 1156-1162. PubMed id: 16211084 DOI: 10.1038/sj.embor.7400550

Date:

08-Aug-16 Release date: 24-Aug-16

Supersedes:

2b2o

Protein chains

Q3JNW6  (KATG_BURP1) -  Catalase-peroxidase from Burkholderia pseudomallei (strain 1710b)

Seq: 728 a.a.

Struc: 713 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.1.11.1.21 - catalase peroxidase.
• Reaction:
  1. H2O2 + AH2 = A + 2 H2O
  2. 2 H2O2 = O2 + 2 H2O

H2O2 + AH2 (Bound ligand (Het Group name = OXY) corresponds exactly) = + 2 × H2O

2 × H2O2 (Bound ligand (Het Group name = OXY) corresponds exactly) = O2 + 2 × H2O

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

reference

DOI no: 10.1038/sj.embor.7400550

EMBO Rep 6:1156-1162 (2005)

PubMed id: 16211084

A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases.

X.Carpena, B.Wiseman, T.Deemagarn, R.Singh, J.Switala, A.Ivancich, I.Fita, P.C.Loewen.

ABSTRACT

The catalase reaction of catalase-peroxidases involves catalase-specific features built into a peroxidase core. An arginine, 20 A from the active-site heme, acts as a molecular switch moving between two conformations, one that activates heme oxidation and one that activates oxoferryl heme reduction by H(2)O(2), facilitating the catalatic pathway in a peroxidase. The influence of the arginine is imparted to the heme through its association with or dissociation from a tyrosinate that modulates reactivity through a Met-Tyr-Trp crosslinked adduct and a pi electron interaction of the heme with the adduct Trp.

Selected figure(s)

Figure 2.
Figure 2 View of the 2F[o]-F[c] electron density maps in the vicinity of Arg 426 modelled at =1.0. (A) BpKatG at pH 5.6 exhibits conformations R and Y at a ratio of approximately 70:30. (B) BpKatG soaked with peroxoacetic acid as in Figure 1 exhibits 100% conformation R. (C) Native BpKatG at pH 8.0 exhibits 100% conformation Y. Panel (D) shows the cavity containing Arg 426 including the two conformations of the Arg 426 side chain.

Figure 5.
Figure 5 Scheme showing changes in electron flux in the adduct and heme under the influence of Arg 426 in conformations Y (A) and R (B). Conformation Y induces electron flux (red arrow) away from the heme, favouring its reduction, whereas conformation R induces electron flux towards the heme, favouring its oxidation.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO Rep (2005, 6, 1156-1162) copyright 2005.

Figures were selected by an automated process.