PDBsum entry 5kqh

Oxidoreductase

PDB id: 5kqh

Contents

Protein chains

713 a.a.

Ligands

HEM ×2

OXY ×2

PO4 ×2

MPD ×4

Metals

_NA ×2

_CL

Waters ×1550

PDB id:

5kqh

Name:

Oxidoreductase

Title:

Crystal structure of the v293d variant of catalase-peroxidase from b. Pseudomallei

Structure:

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

Source:

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

Resolution:

1.82Å R-factor: 0.156 R-free: 0.184

Authors:

P.C.Loewen

Key ref:

M.Machuqueiro et al. (2017). The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Biochemistry, 56, 2271-2281. PubMed id: 28409923 DOI: 10.1021/acs.biochem.6b01276

Date:

06-Jul-16 Release date: 26-Apr-17

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 2 residue positions (black crosses)

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: 10.1021/acs.biochem.6b01276

Biochemistry 56:2271-2281 (2017)

PubMed id: 28409923

The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine.

M.Machuqueiro, B.Victor, J.Switala, J.Villanueva, C.Rovira, I.Fita, P.C.Loewen.

ABSTRACT

The unusual Met-Tyr-Trp adduct composed of cross-linked side chains along with an associated mobile Arg is essential for catalase activity in catalase-peroxidases. In addition, acidic residues in the entrance channel, in particular an Asp and a Glu ∼7 and ∼15 Å, respectively, from the heme, significantly enhance catalase activity. The mechanism by which these channel carboxylates influence catalase activity is the focus of this work. Seventeen new variants with fewer and additional acidic residues have been constructed and characterized structurally and for enzymatic activity, revealing that their effect on activity is roughly inversely proportional to their distance from the heme and adduct, suggesting that the electrostatic potential of the heme cavity may be affected. A discrete group of protonable residues are contained within a 15 Å sphere surrounding the heme iron, and a computational analysis reveals that the pKa of the distal His112, alone, is modulated within the pH range of catalase activity by the remote acidic residues in a pattern consistent with its protonated form having a key role in the catalase reaction cycle. The electrostatic potential also impacts the catalatic reaction through its influence on the charged status of the Met-Tyr-Trp adduct.