Structure of PDB 6r2a Chain A

Receptor sequence

>6r2aA (length=846) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

KNARVIELIAAYRNRGHLMADIDPLRLDLTLWDLDREFKVDGFAGVQRKK
LRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQKY
ILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGLD
EVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHLG
ATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEGS
DNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQIG
FTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQAF
KKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIGR
GDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSKL
ATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAFA
ELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLLA
TNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDFV
NGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQL
WAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVSD
IRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKEN
REDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSFG
LTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG

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: A
• 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	A	H539 R540 Y578 H579 S604 L606 G644 D645 A646 A647 Q651 N678 I680 G681 F682 H747	H158 R159 Y197 H198 S223 L225 G263 D264 A265 A266 Q270 N297 I299 G300 F301 H366
BS02	MG	A	D645 N678 I680	D264 N297 I299
BS03	MG	A	D1004 H1055 D1058 I1060	D623 H674 D677 I679
BS04	ZP1	A	Q901 L950 E952 Q976 F977 F980 H1020	Q520 L569 E571 Q595 F596 F599 H639

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)