Structure of PDB 8p5s Chain A

Receptor sequence

>8p5sA (length=1087) Species: 196627 (Corynebacterium glutamicum ATCC 13032)

PEPGQTPIRGIFKSIAKNMDISLEIPTATSVRDMPARLMFENRAMVNDQL
KRTRGGKISFTHIIGYAMVKAVMAHPDMNNSYDVIDGKPTLIVPEHINLG
LAIDLPQKRALVVAAIKETEKMNFSEFLAAYEDIVARSRKGKLTMDDYQG
VTVSLTNPGGIGTRHSVPRLTKGQGTIIGVGSMDYPAEFQGASEDRLAEL
GVGKLVTITSTYDHRVIQGAVSGEFLRTMSRLLTDDSFWDEIFDAMNVPY
TPMRWAQDVPNTGVDKNTRVMQLIEAYRSRGHLIADTNPLSWVQPGMPVP
DHRDLDIETHNLTIWDLDRTFNVGGFGGKETMTLREVLSRLRAAYTLKVG
SEYTHILDRDERTWLQDRLEAGMPKPTQAEQKYILQKLNAAEAFENFLQT
KYVGQKRFSLEGAEALIPLMDSAIDTAAGQGLDEVVIGMPHRGRLNVLFN
IVGKPLASIFNDVKYHLGSEGQHLQMFGDGEIKVSLTANPSHLEAVNPVM
EGIVRAKQDYLDKGVDGKTVVPLLLHGDAAFAGLGIVPETINLAKLRGYD
VGGTIHIVVNNQIGFTTTPDSSRSMHYATDYAKAFGCPVFHVNGDDPEAV
VWVGQLATEYRRRFGKDVFIDLVCYRLRGHNEADDPSMTQPKMYELITGR
ETVRAQYTEDLLGRGDLSNEDAEAVVRDFHDQMESVFNEVKQKLPHGLET
NISREELLELGQAFANTPEGFNYHPRVAPVAKKRVSSVTEGGIDWAWGEL
LAFGSLANSGRLVRLAGEDSRRGTFTQRHAVAIDPATAEEFNPLHELAQS
KGNNGKFLVYNSALTEYAGMGFEYGYSVGNEDSIVAWEAQFGDFANGAQT
IIDEYVSSGEAKWGQTSKLILLLPHGYEGQGPDHSSARIERFLQLCAEGS
MTVAQPSTPANHFHLLRRHALSDLKRPLVIFTPKSMLRNKAAASAPEDFT
EVTKFQSVINDPNVADAAKVKKVMLVSGKLYYELAKRKEKDGRDDIAIVR
IEMLHPIPFNRISEALAGYPNAEEVLFVQDEPANQGPWPFYQEHLPELIP
NMPKMRRVSRRAQSSTATGVAKVHQLEEKQLIDEAFE

3D structure

• PDB: 8p5s High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
• Chain: A
• Resolution: 2.459 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	COA	A	R142 K156 S158 F159 T160 N259 G261 M285	R43 K57 S59 F60 T61 N157 G159 M183
BS02	ACO	A	P828 H829 G830 T1035 R1051 S1090 M1136 P1139 I1140 P1141 N1143 R1144	P695 H696 G697 T902 R918 S957 M1003 P1006 I1007 P1008 N1010 R1011
BS03	TPP	A	R544 S608 H609 L610 G644 D645 A646 A647 N678 I680 H747	R442 S491 H492 L493 G527 D528 A529 A530 N561 I563 H630
BS04	MG	A	D645 N678 I680	D528 N561 I563

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:8p5s, PDBe:8p5s, PDBj:8p5s
• PDBsum: 8p5s
• PubMed: 37563123
• UniProt: Q8NRC3|ODO12_CORGL 2-oxoglutarate dehydrogenase E1/E2 component (Gene Name=odhA)