SMTL ID : 5esu.1

Crystal Structure of M. tuberculosis MenD bound to Mg2+ and Covalent Intermediate II (a ThDP + de-carboxylated 2-oxoglutarate + Isochorismate adduct)

Coordinates

PDB Format Compare

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.492 Ligands: FMT.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.460, A:D.489, H2O.2 MG.5: 4 residues within 4Å: Chain C: D.460, D.489, G.491 Ligands: TOI.4 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.460, C:D.489, C:G.491, H2O.14 MG.7: 4 residues within 4Å: Chain D: D.460, D.489, G.491 Ligands: TOI.8 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

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

FMT.2: 6 residues within 4Å: Chain A: G.459, D.460, L.461, T.462, G.492 Ligands: MG.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.398, A:D.460, A:L.461, A:T.462, A:T.462 Water bridges: A:T.462 FMT.3: 4 residues within 4Å: Chain B: R.117, G.296, R.297, T.319 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.117 Water bridges: B:T.320, B:T.320, B:T.320

2 x TOI: (1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl (phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1,4-bis(oxidanyl)-4-oxidanylidene-butyl]-6-oxidanyl-5-(3-oxid anyl-3-oxidanylidene-prop-1-en-2-yl)oxy-cyclohex-3-ene-1-carboxylic acid(Non-covalent)

TOI.4: 35 residues within 4Å: Chain B: P.47, G.48, S.49, R.50, E.75, T.98, T.101, A.102, R.127, N.137, Q.138 Chain C: R.302, 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, L.498 Ligands: MG.5 42 PLIP interactions: 25 interactions with chain C, 17 interactions with chain B Hydrophobic interactions: C:I.424, C:I.424, C:L.461, C:F.495, C:F.495, C:L.498, B:P.47, B:T.98 Hydrogen bonds: C:S.397, C:S.397, C:N.398, C:N.398, C:I.424, C:D.460, C:L.461, C:T.462, C:G.493, C:I.494, B:S.49, B:R.50, B:E.75, B:T.98, B:R.127, B:R.127, B:N.137, B:Q.138, B:Q.138 Water bridges: C:R.302, C:R.302, C:R.401, C:R.401, C:R.401, C:G.459, B:S.49, B:R.50, B:R.50, B:E.75, B:A.102 Salt bridges: C:R.302, C:R.401, C:R.419, B:R.127 TOI.8: 35 residues within 4Å: Chain A: P.47, G.48, S.49, R.50, E.75, T.98, T.101, A.102, R.127, N.137, Q.138 Chain D: R.302, 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, L.498 Ligands: MG.7 46 PLIP interactions: 16 interactions with chain A, 30 interactions with chain D Hydrophobic interactions: A:P.47, A:T.98, D:A.422, D:I.424, D:I.424, D:L.461, D:I.494, D:I.494, D:F.495, D:F.495, D:L.498 Hydrogen bonds: A:S.49, A:R.50, A:E.75, A:R.127, A:N.137, A:Q.138, A:Q.138, D:S.397, D:S.397, D:N.398, D:N.398, D:I.424, D:D.460, D:L.461, D:T.462, D:T.462, D:G.493, D:I.494 Water bridges: A:S.49, A:S.49, A:R.50, A:E.75, A:T.101, A:A.102, D:R.401, D:R.401, D:R.401, D:R.401, D:G.459, D:D.489 Salt bridges: A:R.127, D:R.302, D:R.401, D:R.419 pi-Stacking: D:F.495

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.6: 10 residues within 4Å: Chain C: L.45, C.46, E.75, A.78, V.95, A.96, M.97, T.98, A.102, L.106 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.98, C:T.98 BME.9: 9 residues within 4Å: Chain D: L.45, C.46, A.78, V.95, A.96, M.97, T.98, A.102, L.106 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.98

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

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