Structure of PDB 6r2a Chain B

Receptor sequence

>6r2aB (length=855) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

GDSIEDKNARVIELIAAYRNRGHLMADIDPLRLDLDVNSHGLTLWDLDRE
FKVDVQRKKLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHD
KPTVAEQKYILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVI
DQCAEHGLDEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHG
SGDVKYHLGATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQD
LLDTGEEGSDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTI
HIVVNNQIGFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVAR
LAVDFRQAFKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRK
AYTEALIGRGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVE
ADQQIPSKLATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAY
EGRIDWAFAELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGE
EFTPLQLLATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVL
WEAQFGDFVNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTS
GRIERFLQLWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSM
LRNKAAVSDIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYE
LAARKAKENREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPA
NQGAWPSFGLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEIL
DTAFG

3D structure

• PDB: 6r2a Conformational transitions in the active site of mycobacterial 2-oxoglutarate dehydrogenase upon binding phosphonate analogues of 2-oxoglutarate: From a Michaelis-like complex to ThDP adducts.
• Chain: B
• Resolution: 1.7 Å

Enzymatic activity

• Enzyme Commision number: 1.2.4.2: oxoglutarate dehydrogenase (succinyl-transferring).
  2.2.1.5: 2-hydroxy-3-oxoadipate synthase.
  2.3.1.61: dihydrolipoyllysine-residue succinyltransferase.
  4.1.1.71: 2-oxoglutarate decarboxylase.

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	ZP1	B	Q901 L950 E952 Q976 F977 F980 H1020	Q529 L578 E580 Q604 F605 F608 H648
BS02	ZP1	B	H539 R540 Y578 H579 S604 L606 G644 D645 A646 A647 Q651 N678 I680 G681 F682 H747	H167 R168 Y206 H207 S232 L234 G272 D273 A274 A275 Q279 N306 I308 G309 F310 H375
BS03	MG	B	D645 N678 I680	D273 N306 I308
BS04	MG	B	D1004 H1055 D1058 I1060	D632 H683 D686 I688

Gene Ontology

Molecular Function

• GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
• GO:0030976 thiamine pyrophosphate binding

External links

• PDB: RCSB:6r2a, PDBe:6r2a, PDBj:6r2a
• PDBsum: 6r2a
• PubMed: 31476368
• UniProt: A0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)