6R29

Crystal structure of the SucA domain of Mycobacterium smegmatis KGD cocrystallized with succinylphosphonate

Summary for 6R29

• Entry DOI: 10.2210/pdb6r29/pdb
• Descriptor: Multifunctional 2-oxoglutarate metabolism enzyme, (4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-oxidanyl-4-phosphono-butanoic acid, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: oxoglutarate dehydrogenase, tpp-dependent decarboxylase, oxidoreductase
• Biological source: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
• Total number of polymer chains: 2
• Total formula weight: 196238.17

Authors

Wagner, T.,Alzari, P.M.,Bellinzoni, M. (deposition date: 2019-03-15, release date: 2019-09-11, Last modification date: 2024-01-24)

Primary citation

Wagner, T.,Boyko, A.,Alzari, P.M.,Bunik, V.I.,Bellinzoni, M.
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.
J.Struct.Biol., 208:182-190, 2019

PubMed 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 0.043 ± 0.013 mM) than PESP (K 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.

PubMed: 31476368
DOI: 10.1016/j.jsb.2019.08.012

Experimental method

X-RAY DIFFRACTION (1.67 Å)