PDBsum entry 2dv1

Oxidoreductase

PDB id: 2dv1

Contents

Protein chains

714 a.a. *

Ligands

PO4 ×2

HEM ×2

MPD

Metals

_NA ×2

Waters ×1376

* Residue conservation analysis

Superseded by:

5sx1

PDB id:

2dv1

Name:

Oxidoreductase

Title:

Crystal structure of d141e mutant of bpkatg

Structure:

Peroxidase/catalase. Chain: a, b. Synonym: catalase-peroxidase, bpkatg. Engineered: yes. Mutation: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.172 R-free: 0.197

Authors:

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

Key ref:

T.Deemagarn et al. (2007). Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei. Proteins, 66, 219-228. PubMed id: 17063492 DOI: 10.1002/prot.21209

Date:

28-Jul-06 Release date: 07-Nov-06

Protein chains

Q939D2  (KATG_BURPS) -  Catalase-peroxidase from Burkholderia pseudomallei (strain K96243)

Seq: 728 a.a.

Struc: 714 a.a.*

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

DOI no: 10.1002/prot.21209

Proteins 66:219-228 (2007)

PubMed id: 17063492

Two alternative substrate paths for compound I formation and reduction in catalase-peroxidase KatG from Burkholderia pseudomallei.

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

ABSTRACT

Five residues in the multifunctional catalase-peroxidase KatG of Burkholderia pesudomallei are essential for catalase, but not peroxidase, activity. Asp141 is the only one of these catalase-specific residues not related with the covalent adduct found in KatGs that when replaced with a nonacidic residue reduces catalase activity to 5% of native levels. Replacing the nearby catalytic residue Arg108 causes a reduction in catalase activity to 35% of native levels, whereas a variant with both Asp141 and Arg108 replaced exhibits near normal catalase activity (82% of native), suggesting a synergism in the roles of the two residues in support of catalase activity in the enzyme. Among the Asp141 variants, D141E is unique in retaining normal catalase activity but with modified kinetics, suggesting more favorable compound I formation and less favorable compound I reduction. The crystal structure of the D141E variant has been determined at 1.8-A resolution, revealing that the carboxylate of Glu141 is moved only slightly compared with Asp141, but retains its hydrogen bond interaction with the main chain nitrogen of Ile237. In contrast, the low temperature ferric Electron Paramagnetic Resonance spectra of the D141A, R108A, and R108A/D141A variants are consistent with modifications of the water matrix and/or the relative positioning of the distal residue side chains. Such changes explain the reduction in catalase activity in all but the double variant R108A/D141A. Two pathways of hydrogen bonded solvent lead from the entrance channel into the heme active site, one running between Asp141 and Arg108 and the second between Asp141 and the main chain atoms of residues 237-239. It is proposed that binding of substrate H(2)O(2) to Asp141 and Arg108 controls H(2)O(2) access to the heme active site, thereby modulating the catalase reaction.

Selected figure(s)

Figure 1.
Figure 1. (a) Stereo view of the atoms in the heme cavity of native BpKatG. The hydrogen bond interactions of Asp141 with the main chain nitrogen of Ile237 and adjacent waters are shown with dashed lines. The two chains of waters leading into the heme cavity are distinguished by color with the waters in the path leading beside Asp141 and Arg108 colored purple and the waters in the path leading beside Asp141 and residues 237-239 colored green. (b) Diagram showing the solvent molecules in the heme cavity and their hydrogen bond interactions. The diagram is rotated approximately 90° compared with the diagrams in panel (a) and the view is from the top. Waters colored red are situated in the main part of the entrance channel and the division at Asp141 is illustrated with waters colored purple passing by Arg108 and waters colored green passing by the main chain atoms of residues 237-239. Only waters involved in the paths leading to the heme iron are shown.

Figure 4.
Figure 4. Stereo diagrams depicting a series of binding sites for H[2]O[2] entering the heme active site. In panel (a), two substrate molecules are shown bound at sites P1, between Asp141 and Arg108, and P2, among Asp141 and the main chain atoms of residues 238 and 239. In panel (b), the H[2]O[2] has moved so that it is interacting with Arg108 and His112 prior to formation of compound I and water shown in panel (c). The thinner line between the H[2]O[2] and iron in panel (b) denotes a weak interaction that is just starting to form. Panel (d) shows the second H[2]O[2] having moved from P2 to interact with Trp111 and His112 prior to reduction of compound I giving the products shown in panel (e).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 66, 219-228) copyright 2007.

Figures were selected by an automated process.