Structure of PDB 6r29 Chain A

Receptor sequence

>6r29A (length=847) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

DKNARVIELIAAYRNRGHLMADIDPLRLDLTLWDLDREFKVDGFAGVQRK
KLRDILSVLRDAYCRHVGVEYTHILEPEQQRWIQERVETKHDKPTVAEQK
YILSKLNAAEAFETFLQTKYVGQKRFSLEGAETVIPMMDAVIDQCAEHGL
DEVVIAMPHRGRLNVLANIVGKPYSQIFSEFEGNLNPSQAHGSGDVKYHL
GATGTYIQMFGDNDIEVSLTANPSHLEAVDPVLEGLVRAKQDLLDTGEEG
SDNRFSVVPLMLHGDAAFAGQGVVAETLNLALLRGYRTGGTIHIVVNNQI
GFTTAPTDSRSSEYCTDVAKMIGAPIFHVNGDDPEACAWVARLAVDFRQA
FKKDVVIDMLCYRRRGHNEGDDPSMTQPYMYDVIDTKRGSRKAYTEALIG
RGDISMKEAEDALRDYQGQLERVFNEVRELEKHEIEPSESVEADQQIPSK
LATAVDKAMLQRIGDAHLALPEGFTVHPRVRPVLEKRREMAYEGRIDWAF
AELLALGSLIAEGKLVRLSGQDTQRGTFTQRHAVIVDRKTGEEFTPLQLL
ATNPDGTPTGGKFLVYNSALSEFAAVGFEYGYSVGNPDAMVLWEAQFGDF
VNGAQSIIDEFISSGEAKWGQLSDVVLLLPHGHEGQGPDHTSGRIERFLQ
LWAEGSMTIAMPSTPANYFHLLRRHGKDGIQRPLIVFTPKSMLRNKAAVS
DIRDFTESKFRSVLEEPMYTDGEGDRNKVTRLLLTSGKIYYELAARKAKE
NREDVAIVRIEQLAPLPRRRLAETLDRYPNVKEKFWVQEEPANQGAWPSF
GLTLPEILPDHFTGLKRISRRAMSAPSSGSSKVHAVEQQEILDTAFG

3D structure

• PDB: 6r29 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: 1.67 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	QSP	A	H539 R540 Y578 H579 S604 L606 G644 D645 A646 A647 Q651 N678 I680 G681 H747	H159 R160 Y198 H199 S224 L226 G264 D265 A266 A267 Q271 N298 I300 G301 H367
BS02	MG	A	D645 N678 I680	D265 N298 I300
BS03	MG	A	D1004 H1055 D1058 I1060	D624 H675 D678 I680
BS04	QSP	A	Q901 L950 E952 Q976 F980 H1020	Q521 L570 E572 Q596 F600 H640

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:6r29, PDBe:6r29, PDBj:6r29
• PDBsum: 6r29
• PubMed: 31476368
• UniProt: A0R2B1|KGD_MYCS2 Multifunctional 2-oxoglutarate metabolism enzyme (Gene Name=kgd)