PDBsum entry 1qwm

Oxidoreductase

PDB id: 1qwm

Contents

Protein chains

490 a.a. *

Ligands

AZI

HEM-FMT

FMT ×35

HEM

Waters ×933

* Residue conservation analysis

PDB id:

1qwm

Name:

Oxidoreductase

Title:

Structure of helicobacter pylori catalase with formic acid bound

Structure:

Kata catalase. Chain: a, b. Engineered: yes

Source:

Helicobacter pylori. Organism_taxid: 210. Gene: kata (hp0875). Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.60Å R-factor: 0.196 R-free: 0.227

Authors:

P.C.Loewen,X.Carpena,R.Perez-Luque,C.Rovira,R.Haas,S.Odenbreit, P.Nicholls,I.Fita

Key ref:

P.C.Loewen et al. (2004). Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 A resolution. Biochemistry, 43, 3089-3103. PubMed id: 15023060 DOI: 10.1021/bi035663i

Date:

02-Sep-03 Release date: 30-Mar-04

Protein chains

P77872  (CATA_HELPY) -  Catalase from Helicobacter pylori (strain ATCC 700392 / 26695)

Seq: 505 a.a.

Struc: 490 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.11.1.6 - catalase.
• Reaction: 2 H2O2 = O2 + 2 H2O
• Cofactor: Heme; Mn(2+)

Heme (Bound ligand (Het Group name = HEM) matches with 95.45% similarity) Mn(2+)

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

reference

DOI no: 10.1021/bi035663i

Biochemistry 43:3089-3103 (2004)

PubMed id: 15023060

Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 A resolution.

P.C.Loewen, X.Carpena, C.Rovira, A.Ivancich, R.Perez-Luque, R.Haas, S.Odenbreit, P.Nicholls, I.Fita.

ABSTRACT

Helicobacter pylori produces one monofunctional catalase, encoded by katA (hp0875). The crystal structure of H. pylori catalase (HPC) has been determined and refined at 1.6 A with crystallographic agreement factors R and R(free) of 17.4 and 21.9%, respectively. The crystal exhibits P2(1)2(1)2 space group symmetry and contains two protein subunits in the asymmetric unit. The core structure of the HPC subunit, including the disposition of a heme b prosthetic group, is closely related to those of other catalases, although it appears to be the only clade III catalase that has been characterized that does not bind NADPH. The heme iron in one subunit of the native enzyme appears to be covalently modified, possibly with a perhydroxy or dioxygen group in a compound III-like structure. Formic acid is known to bind in the active site of catalases, promoting the breakdown of reaction intermediates compound I and compound II. The structure of an HPC crystal soaked with sodium formate at pH 5.6 has also been determined to 1.6 A (with R and R(free) values of 18.1 and 20.7%, respectively), revealing at least 36 separate formate or formic acid residues in the HPC dimer. In turn, the number of water molecules refined into the models decreased from 1016 in the native enzyme to 938 in the formate-treated enzyme. Extra density, interpreted as azide, is found in a location of both structures that involves interaction with all four subunits in the tetramer. Electron paramagnetic resonance spectra confirm that azide does not bind as a ligand of the iron and that formate does bind in the heme pocket. The stability of the formate or formic acid molecule found inside the heme distal pocket has been investigated by calculations based on density functional theory.