Structure of PDB 8p5v Chain D

Receptor sequence

>8p5vD (length=1121) Species: 196627 (Corynebacterium glutamicum ATCC 13032)

PEPGQTPIRGIFKSIAKNMDISLEIPTATSVRDMPARLMFENRAMVNDQL
KRTRGGKISFTHIIGYAMVKAVMAHPDMNNSYDVIDGKPTLIVPEHINLG
LAIDLPQKDGSRALVVAAIKETEKMNFSEFLAAYEDIVARSRKGKLTMDD
YQGVTVSLTNPGGIGTRHSVPRLTKGQGTIIGVGSMDYPAEFQGASEDRL
AELGVGKLVTITSTYDHRVIQGAVSGEFLRTMSRLLTDDSFWDEIFDAMN
VPYTPMRWAQDVPNTGVDKNTRVMQLIEAYRSRGHLIADTNPLSWVQPGM
PVPDHRDLDIETHNLTIWDLDRTFNVGGFGGKETMTLREVLSRLRAAYTL
KVGSEYTHILDRDERTWLQDRLEAGMPKPTQAEQKYILQKLNAAEAFENF
LQTKYVGQKRFSLEGAEALIPLMDSAIDTAAGQGLDEVVIGMPHRGRLNV
LFNIVGKPLASIFNEFEGQMEQGQIGGSGDVKYHLGSEGQHLQMFGDGEI
KVSLTANPSHLEAVNPVMEGIVRAKQDYLDKGVDGKTVVPLLLHGDAAFA
GLGIVPETINLAKLRGYDVGGTIHIVVNNQIGFTTTPDSSRSMHYATDYA
KAFGCPVFHVNGDDPEAVVWVGQLATEYRRRFGKDVFIDLVCYRLRGHNE
ADDPSMTQPKMYELITGRETVRAQYTEDLLGRGDLSNEDAEAVVRDFHDQ
MESVFNEVKEGGKKQAEAQTGITGSQKLPHGLETNISREELLELGQAFAN
TPEGFNYHPRVAPVAKKRVSSVTEGGIDWAWGELLAFGSLANSGRLVRLA
GEDSRRGTFTQRHAVAIDPATAEEFNPLHELAQSKGNNGKFLVYNSALTE
YAGMGFEYGYSVGNEDSIVAWEAQFGDFANGAQTIIDEYVSSGEAKWGQT
SKLILLLPHGYEGQGPDHSSARIERFLQLCAEGSMTVAQPSTPANHFHLL
RRHALSDLKRPLVIFTPKSMLRNKAAASAPEDFTEVTKFQSVINDPNVAD
AAKVKKVMLVSGKLYYELAKRKEKDGRDDIAIVRIEMLHPIPFNRISEAL
AGYPNAEEVLFVQDEPANQGPWPFYQEHLPELIPNMPKMRRVSRRAQSST
ATGVAKVHQLEEKQLIDEAFE

3D structure

• PDB: 8p5v High resolution cryo-EM and crystallographic snapshots of the actinobacterial two-in-one 2-oxoglutarate dehydrogenase.
• Chain: D
• Resolution: 2.07 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	SCA	D	S129 Y314	S30 Y215
BS02	TPP	D	E949 F977	E850 F878
BS03	MG	D	D645 N678 I680	D546 N579 I581
BS04	ACO	D	T822 P828 H829 G830 G1032 T1035 R1051 L1057 K1087 S1090 M1136 P1139 I1140 P1141 F1142 N1143 R1144	T723 P729 H730 G731 G933 T936 R952 L958 K988 S991 M1037 P1040 I1041 P1042 F1043 N1044 R1045
BS05	TPP	D	H543 R544 S608 L610 G644 A646 A647 N678 I680 H747	H444 R445 S509 L511 G545 A547 A548 N579 I581 H648
BS06	SCA	D	R142 K156 S158 F159 T160 Y233 T258 N259 G261 S268 P270 M285	R43 K57 S59 F60 T61 Y134 T159 N160 G162 S169 P171 M186

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:8p5v, PDBe:8p5v, PDBj:8p5v
• PDBsum: 8p5v
• PubMed: 37563123
• UniProt: Q8NRC3|ODO12_CORGL 2-oxoglutarate dehydrogenase E1/E2 component (Gene Name=odhA)