Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 4851, Year 2023
Publish date	Aug 10, 2023
Authors	Lu Yang / Tristan Wagner / Ariel Mechaly / Alexandra Boyko / Eduardo M Bruch / Daniela Megrian / Francesca Gubellini / Pedro M Alzari / Marco Bellinzoni /
PubMed Abstract	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 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.
External links	Nat Commun / PubMed:37563123 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.07 - 4.562 Å
Structure data	17452 8p5t EMDB-17452, PDB-8p5t: Single particle cryo-EM structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum Method: EM (single particle) / Resolution: 2.17 Å 17453 8p5u EMDB-17453, PDB-8p5u: Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum with Coenzyme A bound to the E2o domain Method: EM (single particle) / Resolution: 2.17 Å 17454 8p5v EMDB-17454, PDB-8p5v: Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum in complex with the product succinyl-CoA Method: EM (single particle) / Resolution: 2.07 Å 17455 8p5w EMDB-17455, PDB-8p5w: Single particle cryo-EM structure of homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum following reaction with the 2-oxoglutarate analogue succinyl phosphonate Method: EM (single particle) / Resolution: 2.26 Å 17456 8p5x EMDB-17456, PDB-8p5x: Single particle cryo-EM structure of the complex between Corynebacterium glutamicum homohexameric 2-oxoglutarate dehydrogenase OdhA and the FHA-protein inhibitor OdhI Method: EM (single particle) / Resolution: 2.29 Å PDB-8p5r: Crystal structure of full-length, homohexameric 2-oxoglutarate dehydrogenase KGD from Mycobacterium smegmatis in complex with GarA Method: X-RAY DIFFRACTION / Resolution: 4.562 Å PDB-8p5s: Crystal structure of the homohexameric 2-oxoglutarate dehydrogenase OdhA from Corynebacterium glutamicum Method: X-RAY DIFFRACTION / Resolution: 2.459 Å
Chemicals	ChemComp-MG: Unknown entry ChemComp-CA: Unknown entry ChemComp-TPP: THIAMINE DIPHOSPHATE / Thiamine pyrophosphate ChemComp-EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH bufferYM / HEPES ChemComp-COA: COENZYME A / Coenzyme A ChemComp-ACO: ACETYL COENZYME A / Acetyl-CoA ChemComp-HOH: WATER / Water ChemComp-SCA: SUCCINYL-COENZYME A / Succinyl-CoA ChemComp-QSP: (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
Source	corynebacterium glutamicum atcc 13032 (bacteria) mycolicibacterium smegmatis mc2 155 (bacteria)
Keywords	OXIDOREDUCTASE / 2-oxoglutarate dehydrogenase; ODH; KGD; OXIDOREDUCTASE / 2-oxoglutarate dehydrogenase; ODH