PDBsum entry: 2fxh

Oxidoreductase

PDB id: 2fxh

Contents

Protein chains

715 a.a. *

Ligands

HEM ×2

TRS ×4

MPD

Metals

_NA ×2

Waters ×1549

* Residue conservation analysis

PDB id:

2fxh

Name:

Oxidoreductase

Title:

Crystal structure of katg at ph 6.5

Structure:

Catalase-peroxidase protein. Chain: a, b. Engineered: yes

Source:

Burkholderia pseudomallei. Organism_taxid: 28450. Gene: katg. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.150 R-free: 0.177

Authors:

X.Carpena,B.Wiseman,T.Deemagarn,B.Herguedas,A.Ivancich,R.Sin P.C.Loewen,I.Fita

Key ref:

X.Carpena et al. (2006). Roles for Arg426 and Trp111 in the modulation of NADH oxidase activity of the catalase-peroxidase KatG from Burkholderia pseudomallei inferred from pH-induced structural changes. Biochemistry, 45, 5171-5179. PubMed id: 16618106 DOI: 10.1021/bi060017f

Date:

06-Feb-06 Release date: 06-Mar-07

Protein chains

Q939D2  (KATG_BURPS) -  Catalase-peroxidase

Seq: 728 a.a.

Struc: 715 a.a.

Enzyme reactions

• Enzyme class: E.C.1.11.1.21 - Catalase peroxidase.
• Reaction:
  1. Donor + H₂O₂ = oxidized donor + 2 H₂O
  2. 2 H₂O₂ = O₂ + 2 H₂O

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

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: oxidoreductase activity (5 terms)

reference

DOI no: 10.1021/bi060017f

Biochemistry 45:5171-5179 (2006)

PubMed id: 16618106

Roles for Arg426 and Trp111 in the modulation of NADH oxidase activity of the catalase-peroxidase KatG from Burkholderia pseudomallei inferred from pH-induced structural changes.

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

ABSTRACT

Crystals of Burkholderia pseudomallei KatG retain their ability to diffract X-rays at high resolution after adjustment of the pH from 5.6 to 4.5, 6.5, 7.5, and 8.5, providing a unique view of the effect of pH on protein structure. One significant pH-sensitive change lies in the appearance of a perhydroxy group attached to the indole nitrogen of the active site Trp111 above pH 7, similar to a modification originally observed in the Ser324Thr variant of the enzyme at pH 5.6. The modification forms rapidly from molecular oxygen in the buffer with 100% occupancy after one minute of soaking of the crystal at room temperature and pH 8.5. The low temperature (4 K) ferric EPR spectra of the resting enzyme, being very sensitive to changes in the heme iron microenvironment, confirm the presence of the modification above pH 7 in native enzyme and variants lacking Arg426 or Met264 and its absence in variants lacking Trp111 or Tyr238. The indole-perhydroxy group is very likely the reactive intermediate of molecular oxygen in the NADH oxidase reaction, and Arg426 is required for its reduction. The second significant pH-sensitive change involves the buried side chain of Arg426 that changes from one predominant conformation at low pH to a second at high pH. The pH profiles of the peroxidase, catalase, and NADH oxidase reactions can be correlated with the distribution of Arg426 conformations. Other pH-induced structural changes include a number of surface-situated side chains, but there is only one change involving a displacement of main chain atoms triggered by the protonation of His53 in a deep pocket in the vicinity of the molecular 2-fold axis.