8P5W image
Deposition Date 2023-05-24
Release Date 2023-08-16
Last Version Date 2023-08-23
Entry Detail
PDB ID:
8P5W
Keywords:
Title:
Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum following reaction with the 2-oxoglutarate analogue succinyl phosphonate
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.26 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:2-oxoglutarate dehydrogenase E1/E2 component
Gene (Uniprot):odhA
Chain IDs:A, B, C, D, E, F
Chain Length:1223
Number of Molecules:6
Biological Source:Corynebacterium glutamicum ATCC 13032
Primary Citation
High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
Nat Commun 14 4851 4851 (2023)
PMID: 37563123 DOI: 10.1038/s41467-023-40253-6

Abstact

Actinobacteria possess unique ways to regulate the oxoglutarate metabolic node. Contrary to most organisms in which three enzymes compose the 2-oxoglutarate dehydrogenase complex (ODH), actinobacteria rely on a two-in-one protein (OdhA) in which both the oxidative decarboxylation and succinyl transferase steps are carried out by the same polypeptide. Here we describe high-resolution cryo-EM and crystallographic snapshots of representative enzymes from Mycobacterium smegmatis and Corynebacterium glutamicum, showing that OdhA is an 800-kDa homohexamer that assembles into a three-blade propeller shape. The obligate trimeric and dimeric states of the acyltransferase and dehydrogenase domains, respectively, are critical for maintaining the overall assembly, where both domains interact via subtle readjustments of their interfaces. Complexes obtained with substrate analogues, reaction products and allosteric regulators illustrate how these domains operate. Furthermore, we provide additional insights into the phosphorylation-dependent regulation of this enzymatic machinery by the signalling protein OdhI.

Legend

Protein

Chemical

Disease

Primary Citation of related structures