Database: EMDB / ID: EMD-26649
|Title||Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney|
|Function / homology|
Function and homology information
histone succinylation / succinyl-CoA metabolic process / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / L-lysine catabolic process to acetyl-CoA via saccharopine / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / acyltransferase activity / tricarboxylic acid cycle / mitochondrial matrix ...histone succinylation / succinyl-CoA metabolic process / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / L-lysine catabolic process to acetyl-CoA via saccharopine / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / acyltransferase activity / tricarboxylic acid cycle / mitochondrial matrix / mitochondrion / nucleus
Similarity search - Function
Dihydrolipoamide succinyltransferase / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
Similarity search - Component
|Biological species||Bos taurus (cattle) / cattle (cattle)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.5 Å|
|Authors||Liu S / Xia X / Zhen J / Li ZH / Zhou ZH|
|Funding support|| United States, 3 items |
|Citation||Journal: Cell Discov / Year: 2022|
Title: Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney.
Authors: Shiheng Liu / Xian Xia / James Zhen / Zihang Li / Z Hong Zhou /
Abstract: The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members ...The α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in native states remain unknown. Here, we report the cryo-electron microscopy structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at resolutions of 3.5 Å and 3.8 Å, respectively. The structures of multiple proteins were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, the native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. In addition, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the twofold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides a direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.
Downloads & links
|File||Download / File: emd_26649.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.36 Å|
|Symmetry||Space group: 1|
|Projections & Slices|
-Half map: #2
|Projections & Slices|
-Half map: #1
-Entire : Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-ox...
|Entire||Name: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney|
-Supramolecule #1: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-ox...
|Supramolecule||Name: Endogenous dihydrolipoamide succinyltransferase (E2) core of 2-oxoglutarate dehydrogenase complex from bovine kidney|
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
|Source (natural)||Organism: Bos taurus (cattle) / Organ: kidney / Tissue: kidney / Organelle: mitochondria / Location in cell: mitochondrial matrix|
|Molecular weight||Theoretical: 49 KDa|
-Macromolecule #1: Dihydrolipoyllysine-residue succinyltransferase component of 2-ox...
|Macromolecule||Name: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial|
type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: dihydrolipoyllysine-residue succinyltransferase
|Source (natural)||Organism: cattle (cattle) / Organ: kidney / Tissue: kidney|
|Molecular weight||Theoretical: 49.034414 KDa|
|Sequence||String: MLSRSRCASR AFSRSLSAFQ KGNCPLVRRS LPGISLCQGP GYPDSRKTVI NSSNIFSVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAAA P AAAAPKAE ...String: |
MLSRSRCASR AFSRSLSAFQ KGNCPLVRRS LPGISLCQGP GYPDSRKTVI NSSNIFSVRF FRTTAVCKDD VITVKTPAFA ESVTEGDVR WEKAVGDTVA EDEVVCEIET DKTSVQVPSP ANGVIEALLV PDGGKVEGGT PLFTLRKTGA APAKAKPAAA P AAAAPKAE PTVSAVPPPP AAPIPTQMPP VPSPSQPLTS KPVSAVKPTA APPRAEAGAG VGLRSEHREK MNRMRQRIAQ RL KEAQNTC AMLTTFNEID MSNIQEMRAR HKDAFLKKHN LKLGFMSAFV KASAFALQEQ PVVNAVIDDA TKEVVYRDYI DIS VAVATP RGLVVPVIRN VETMNYADIE RTISELGEKA RKNELAIEDM DGGTFTISNG GVFGSLFGTP IINPPQSAIL GMHA IVDRP VVIGGKVEVR PMMYVALTYD HRLIDGREAV TFLRKIKAAV EDPRVLLLDL
|Processing||single particle reconstruction|
|Grid||Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE|
|Vitrification||Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV|
|Microscope||FEI TITAN KRIOS|
|Electron beam||Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 105000|
|Sample stage||Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN|
|Image recording||Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 45.0 e/Å2|
Model: Titan Krios / Image courtesy: FEI Company
-Atomic model buiding 1
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