PDBsum entry 6r2c

Oxidoreductase

PDB id: 6r2c

Contents

Protein chains

814 a.a.

Ligands

TPP ×4

JQ5 ×4

Metals

_MG ×4

_CA ×4

Waters ×847

References listed in PDB file

Key reference

• Title: Conformational transitions in the active site of mycobacterial 2-Oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-Oxoglutarate: from a michaelis-Like complex to thdp adducts.
• Authors: T.Wagner, A.Boyko, P.M.Alzari, V.I.Bunik, M.Bellinzoni.
• Ref.: J Struct Biol, 2019, 208, 182-190. [DOI no: 10.1016/j.jsb.2019.08.012]
• PubMed id: 31476368

Abstract

Mycobacterial KGD, the thiamine diphosphate (ThDP)-dependent E1o component of the 2-oxoglutarate dehydrogenase complex (OGDHC), is known to undergo significant conformational changes during catalysis with two distinct conformational states, previously named as the early and late state. In this work, we employ two phosphonate analogues of 2-oxoglutarate (OG), i.e. succinyl phosphonate (SP) and phosphono ethyl succinyl phosphonate (PESP), as tools to isolate the first catalytic steps and understand the significance of conformational transitions for the enzyme regulation. The kinetics showed a more efficient inhibition of mycobacterial E1o by SP (K_i 0.043 ± 0.013 mM) than PESP (K_i 0.88 ± 0.28 mM), consistent with the different circular dichroism spectra of the corresponding complexes. PESP allowed us to get crystallographic snapshots of the Michaelis-like complex, the first one for 2-oxo acid dehydrogenases, followed by the covalent adduction of the inhibitor to ThDP, mimicking the pre-decarboxylation complex. In addition, covalent ThDP-phosphonate complexes obtained with both compounds by co-crystallization were in the late conformational state, probably corresponding to slowly dissociating enzyme-inhibitor complexes. We discuss the relevance of these findings in terms of regulatory features of the mycobacterial E1o enzymes, and in the perspective of developing tools for species-specific metabolic regulation.