SMTL ID : 5ess.1

Crystal Structure of M. tuberculosis MenD bound to Mg2+ and covalent intermediate I (a ThDP and decarboxylated 2-oxoglutarate adduct)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.460, D.489, G.491 Ligands: DPO.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.460, A:D.489, A:G.491 MG.12: 5 residues within 4Å: Chain C: D.460, D.489, G.491, G.493 Ligands: TOG.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.460, C:D.489, C:G.491, H2O.13 MG.16: 5 residues within 4Å: Chain D: D.460, D.489, G.491, G.493 Ligands: TOG.15 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.460, D:D.489, D:G.491, H2O.18

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 4 residues within 4Å: Chain A: E.160, A.162, P.163, T.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.162, A:A.162 FMT.3: 5 residues within 4Å: Chain A: T.270, I.413, R.414, V.415, R.416 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.413, A:V.415, A:R.416 FMT.4: 5 residues within 4Å: Chain A: L.367, A.368, H.370, L.372, H.377 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.368 FMT.5: 6 residues within 4Å: Chain A: G.48, S.49, R.50, T.98, Q.138 Ligands: TOG.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.49, A:R.50, A:T.98, A:Q.138 FMT.7: 4 residues within 4Å: Chain B: E.160, A.162, T.166, W.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.162, B:T.166 FMT.8: 5 residues within 4Å: Chain B: T.270, I.413, R.414, V.415, R.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.415, B:R.416 FMT.9: 6 residues within 4Å: Chain B: G.48, S.49, R.50, T.98, Q.138 Ligands: TOG.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.49, B:R.50, B:Q.138 FMT.13: 4 residues within 4Å: Chain C: T.270, I.413, V.415, R.416 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.415, C:R.416 FMT.14: 2 residues within 4Å: Chain C: R.414, R.416 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.414, C:R.416, C:R.416 FMT.17: 6 residues within 4Å: Chain D: T.265, V.266, A.267, R.273, P.278, L.279 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.265, D:A.267, D:L.279

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.6: 10 residues within 4Å: Chain A: N.398, G.459, D.460, L.461, T.462, D.489, G.491, G.492, G.493 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.397, A:N.398, A:L.461, A:T.462, A:T.462, A:G.493 Water bridges: A:G.459, A:G.459

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain B: T.265, V.266, A.267, R.273, P.278, L.279, P.281 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.265, B:A.267

2 x TOG: 4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3 -ium-2-yl]-4-oxidanyl-butanoic acid(Non-covalent)

TOG.11: 29 residues within 4Å: Chain B: P.47, E.75, T.98, T.101, A.102, N.137, Q.138 Chain C: A.396, S.397, N.398, P.399, R.401, R.419, A.422, G.423, I.424, D.425, G.459, D.460, L.461, T.462, D.489, G.491, G.492, G.493, I.494, F.495 Ligands: FMT.9, MG.12 25 PLIP interactions: 20 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:A.422, C:I.424, C:L.461, B:P.47, B:T.98 Hydrogen bonds: C:S.397, C:S.397, C:N.398, C:N.398, C:A.422, C:I.424, C:D.460, C:L.461, C:T.462, C:T.462, C:G.493, C:I.494, B:N.137 Water bridges: C:G.459, C:D.460, B:T.101, B:A.102 Salt bridges: C:R.401, C:R.419 pi-Stacking: C:F.495 TOG.15: 30 residues within 4Å: Chain A: P.47, E.75, T.98, T.101, A.102, N.137, Q.138 Chain D: A.396, S.397, N.398, P.399, R.401, R.419, A.422, G.423, I.424, D.425, G.459, D.460, L.461, T.462, H.465, D.489, G.491, G.492, G.493, I.494, F.495 Ligands: FMT.5, MG.16 27 PLIP interactions: 23 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:I.424, D:I.424, D:D.425, D:L.461, D:F.495, A:P.47, A:T.98 Hydrogen bonds: D:S.397, D:S.397, D:N.398, D:N.398, D:A.422, D:I.424, D:G.459, D:D.460, D:D.460, D:L.461, D:T.462, D:D.489, D:G.493, D:I.494, A:N.137 Water bridges: D:T.462, A:A.102 Salt bridges: D:R.401, D:R.419 pi-Stacking: D:F.495

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.18: 5 residues within 4Å: Chain D: T.270, I.413, R.414, V.415, R.416 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.415 Water bridges: D:R.416 Salt bridges: D:R.416 ACT.19: 3 residues within 4Å: Chain D: T.373, A.558, D.559 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.373 ACT.20: 1 residues within 4Å: Chain D: I.36 2 PLIP interactions: 2 interactions with chain D Water bridges: D:I.36, D:G.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jirgis, E.N. et al., Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms. Structure (2016)

Release Date

2016-06-22

Peptides

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Related Entries With Identical Sequence