Structure of PDB 8p5u Chain D

Receptor sequence

>8p5uD (length=1119) Species: 196627 (Corynebacterium glutamicum ATCC 13032)

PGQTPIRGIFKSIAKNMDISLEIPTATSVRDMPARLMFENRAMVNDQLKR
TRGGKISFTHIIGYAMVKAVMAHPDMNNSYDVIDGKPTLIVPEHINLGLA
IDLPQKDGSRALVVAAIKETEKMNFSEFLAAYEDIVARSRKGKLTMDDYQ
GVTVSLTNPGGIGTRHSVPRLTKGQGTIIGVGSMDYPAEFQGASEDRLAE
LGVGKLVTITSTYDHRVIQGAVSGEFLRTMSRLLTDDSFWDEIFDAMNVP
YTPMRWAQDVPNTGVDKNTRVMQLIEAYRSRGHLIADTNPLSWVQPGMPV
PDHRDLDIETHNLTIWDLDRTFNVGGFGGKETMTLREVLSRLRAAYTLKV
GSEYTHILDRDERTWLQDRLEAGMPKPTQAEQKYILQKLNAAEAFENFLQ
TKYVGQKRFSLEGAEALIPLMDSAIDTAAGQGLDEVVIGMPHRGRLNVLF
NIVGKPLASIFNEFEGQMEQGQIGGSGDVKYHLGSEGQHLQMFGDGEIKV
SLTANPSHLEAVNPVMEGIVRAKQDYLDKGVDGKTVVPLLLHGDAAFAGL
GIVPETINLAKLRGYDVGGTIHIVVNNQIGFTTTPDSSRSMHYATDYAKA
FGCPVFHVNGDDPEAVVWVGQLATEYRRRFGKDVFIDLVCYRLRGHNEAD
DPSMTQPKMYELITGRETVRAQYTEDLLGRGDLSNEDAEAVVRDFHDQME
SVFNEVKEGGKKQAEAQTGITGSQKLPHGLETNISREELLELGQAFANTP
EGFNYHPRVAPVAKKRVSSVTEGGIDWAWGELLAFGSLANSGRLVRLAGE
DSRRGTFTQRHAVAIDPATAEEFNPLHELAQSKGNNGKFLVYNSALTEYA
GMGFEYGYSVGNEDSIVAWEAQFGDFANGAQTIIDEYVSSGEAKWGQTSK
LILLLPHGYEGQGPDHSSARIERFLQLCAEGSMTVAQPSTPANHFHLLRR
HALSDLKRPLVIFTPKSMLRNKAAASAPEDFTEVTKFQSVINDPNVADAA
KVKKVMLVSGKLYYELAKRKEKDGRDDIAIVRIEMLHPIPFNRISEALAG
YPNAEEVLFVQDEPANQGPWPFYQEHLPELIPNMPKMRRVSRRAQSSTAT
GVAKVHQLEEKQLIDEAFE

3D structure

• PDB: 8p5u High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
• Chain: D
• Resolution: 2.17 Å

Enzymatic activity

• Enzyme Commision number: 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
  2.3.1.61: dihydrolipoyllysine-residue succinyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	TPP	D	E901 L947 E949 Q973 F977	E800 L846 E848 Q872 F876
BS02	MG	D	D645 N678 I680	D544 N577 I579
BS03	COA	D	Y233 E234 N259 G261 M285	Y132 E133 N158 G160 M184
BS04	ACO	D	P828 G830 G1032 T1035 R1051 P1139 I1140 P1141 F1142 N1143 R1144	P727 G729 G931 T934 R950 P1038 I1039 P1040 F1041 N1042 R1043
BS05	TPP	D	R544 L610 A646 A647 N678 I680 H747	R443 L509 A545 A546 N577 I579 H646

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004149 dihydrolipoyllysine-residue succinyltransferase activity
• GO:0004591 oxoglutarate dehydrogenase (succinyl-transferring) activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
• GO:0016746 acyltransferase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006099 tricarboxylic acid cycle

Cellular Component

• GO:0005829 cytosol
• GO:0045252 oxoglutarate dehydrogenase complex

External links

• PDB: RCSB:8p5u, PDBe:8p5u, PDBj:8p5u
• PDBsum: 8p5u
• PubMed: 37563123
• UniProt: Q8NRC3|ODO12_CORGL 2-oxoglutarate dehydrogenase E1/E2 component (Gene Name=odhA)