PDBsum entry: 1u2k

Oxidoreductase

PDB id: 1u2k

Contents

Protein chain

292 a.a. *

Waters ×93

* Residue conservation analysis

PDB id:

1u2k

Name:

Oxidoreductase

Title:

Crystal structure of thE C-terminal domain from the catalase peroxidase katg of escherichia coli (i41)

Structure:

Peroxidase/catalase hpi. Chain: a. Fragment: c-terminal domain. Synonym: catalase-peroxidase, hydroperoxidase i. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: katg. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.192 R-free: 0.249

Authors:

X.Carpena,W.Melik-Adamyan,P.C.Loewen,I.Fita

Key ref:

X.Carpena et al. (2004). Structure of the C-terminal domain of the catalase-peroxidase KatG from Escherichia coli. Acta Crystallogr D Biol Crystallogr, 60, 1824-1832. PubMed id: 15388929 DOI: 10.1107/S0907444904020621

Date:

19-Jul-04 Release date: 05-Oct-04

Protein chain

P13029  (KATG_ECOLI) -  Catalase-peroxidase

Seq: 726 a.a.

Struc: 292 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 (2 terms)
• Biochemical function: peroxidase activity (2 terms)

reference

DOI no: 10.1107/S0907444904020621

Acta Crystallogr D Biol Crystallogr 60:1824-1832 (2004)

PubMed id: 15388929

Structure of the C-terminal domain of the catalase-peroxidase KatG from Escherichia coli.

X.Carpena, W.Melik-Adamyan, P.C.Loewen, I.Fita.

ABSTRACT

Catalase-peroxidases or KatGs, the apparent in vivo activators of the anti-tubercular pro-drug isoniazid, are active as homodimers, each subunit having two distinct but sequence- and structure-related domains. The N-terminal domain contains the haem group and is catalytically active, while the C-terminal domain lacks the cofactor. The C-terminal domain of KatG from Escherichia coli is expressed as a soluble protein which has been crystallized in triclinic, orthorhombic and tetragonal crystal forms. Packing in the orthorhombic crystals, with eight molecules in the asymmetric unit, follows the pattern of commensurate modulated structures, which explains the diversity of pseudo-origin peaks observed in the native Patterson map. The different crystal forms arise from variations in the length and sequence of the N-terminal extensions in the different constructs. Despite the variability in the N-terminal region, the overall domain conformations beginning with Pro437 are very similar both to each other and to the C-terminal domains within the native structures of the KatGs from Haloarcula marismortui and Burkholderia pseudomallei. Some structural reorganization in the C-terminal domain relative to the N-terminal domain has evolved to compensate for the absence of the haem group. A high percentage of the residues in the C-terminal domains of KatG proteins from different sources are highly conserved and these residues are spread uniformly throughout the domain. The easily folded nature and retention of structure in the C-terminal domain suggests that it may serve as a platform for the folding of the N-terminal domain and for stabilization of the molecular dimer.

Selected figure(s)

Figure 3.
Figure 3 Stereo image of the superimposition of a single subunit from each of the three EcKatG C-terminal domain space groups (P2[1]2[1]2[1] in gold, P1 in blue and I4[1] in green) and the C-terminal domain of BpKatG (in red). Pro437, the apparent beginning of the globular domain, is indicated. The asterisk indicates the loop that differs in the P1 subunit compared with all the others.

Figure 7.
Figure 7 Stereo images showing the organization in the region of EcKatG C-terminal domain that is equivalent to the haem cavity in the N-terminal domain. In (a), the electron density in the region has the EcKatG C-domain model as refined superimposed on it. In (b), the distal-side catalytic residues and haem from the N-terminal domain of BpKatG are superimposed on the density to illustrate the differences between the two cavities, but also to illustrate how some of the C-terminal residues are situated to compensate for the absence of the haem or the catalytic residues. In comparing the three distal-side catalytic residues, the arginine is replaced by serine (Ser469) and the active-site histidine is replaced by Ala473. Only the active-site tryptophan is retained as Trp472.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1824-1832) copyright 2004.

Figures were selected by an automated process.