5L05

Crystal structure of catalase-peroxidase KATG of burkholderia pseudomallei treated with INH

Replaces:  1MWV

Summary for 5L05

• Entry DOI: 10.2210/pdb5l05/pdb
• Related: 5L02 5SW4 5SW5 5SW6 5SX0 5SX1 5SX2 5SX3 5SX6 5SX7 5SXQ 5SXR 5SXS 5SXT 5SXX 5SYH 5SYI 5SYJ 5SYK 5SYL 5SYU 5SYV 5SYW 5SYX 5SYY
• Descriptor: Catalase-peroxidase, Peroxidized Heme Form 2, SODIUM ION, ... (6 entities in total)
• Functional Keywords: catalase, peroxidase, katg, oxidoreductase
• Biological source: Burkholderia pseudomallei (strain 1710b)
• Total number of polymer chains: 2
• Total formula weight: 160835.44

Authors

Loewen, P.C. (deposition date: 2016-07-26, release date: 2016-08-24, Last modification date: 2024-10-30)

Primary citation

Carpena, X.,Loprasert, S.,Mongkolsuk, S.,Switala, J.,Loewen, P.C.,Fita, I.
Catalase-peroxidase KatG of Burkholderia pseudomallei at 1.7A resolution.
J. Mol. Biol., 327:475-489, 2003

PubMed Abstract: The catalase-peroxidase encoded by katG of Burkholderia pseudomallei (BpKatG) is 65% identical with KatG of Mycobacterium tuberculosis, the enzyme responsible for the activation of isoniazid as an antibiotic. The structure of a complex of BpKatG with an unidentified ligand, has been solved and refined at 1.7A resolution using X-ray synchrotron data collected from crystals flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are 15.3% and 18.6%, respectively. The crystallized enzyme is a dimer with one modified heme group and one metal ion, likely sodium, per subunit. The modification on the heme group involves the covalent addition of two or three atoms, likely a perhydroxy group, to the secondary carbon atom of the vinyl group on ring I. The added group can form hydrogen bonds with two water molecules that are also in contact with the active-site residues Trp111 and His112, suggesting that the modification may have a catalytic role. The heme modification is in close proximity to an unusual covalent adduct among the side-chains of Trp111, Tyr238 and Met264. In addition, Trp111 appears to be oxidized on C(delta1) of the indole ring. The main channel, providing access of substrate hydrogen peroxide to the heme, contains a region of unassigned electron density consistent with the binding of a pyridine nucleotide-like molecule. An interior cavity, containing the sodium ion and an additional region of unassigned density, is evident adjacent to the adduct and is accessible to the outside through a second funnel-shaped channel. A large cleft in the side of the subunit is evident and may be a potential substrate-binding site with a clear pathway for electron transfer to the active-site heme group through the adduct.

PubMed: 12628252

Experimental method

X-RAY DIFFRACTION (1.7 Å)