SMTL ID : 3oe1.1

Pyruvate decarboxylase variant Glu473Asp from Z. mobilis in complex with reaction intermediate 2-lactyl-ThDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.440, N.467, G.469 Ligands: TDL.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.440, A:G.469, H2O.14 MG.3: 6 residues within 4Å: Chain B: D.440, G.441, I.465, N.467, G.469 Ligands: TDL.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.440, B:G.469, H2O.22 MG.5: 4 residues within 4Å: Chain C: D.440, N.467, G.469 Ligands: TDL.6 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.440, C:G.469, H2O.37 MG.7: 4 residues within 4Å: Chain D: D.440, N.467, G.469 Ligands: TDL.8 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.440, D:G.469, H2O.46

4 x TDL: 3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM(Non-covalent)

TDL.2: 27 residues within 4Å: Chain A: Y.290, T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, D.473, I.476 Chain B: A.25, G.26, D.27, E.50, T.72, V.75, H.114 Ligands: MG.1 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.388, A:L.445, A:Y.470, A:I.472 Hydrogen bonds: A:D.390, A:G.413, A:I.415, A:G.439, A:G.439, A:G.441, A:S.442, A:N.467, A:N.467, A:T.471, A:T.471, A:I.472, A:D.473, B:D.27 Water bridges: A:S.391, A:D.440, A:S.442, A:S.442, B:D.27, B:Y.28 TDL.4: 27 residues within 4Å: Chain A: A.25, G.26, D.27, E.50, T.72, V.75, H.113, H.114 Chain B: Y.290, T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, D.473 Ligands: MG.3 29 PLIP interactions: 23 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:T.388, B:I.415, B:I.415, B:L.445, B:I.472, B:I.472, A:V.75 Hydrogen bonds: B:D.390, B:G.413, B:G.413, B:I.415, B:G.439, B:G.439, B:G.441, B:S.442, B:N.467, B:N.467, B:T.471, B:T.471, B:T.471, B:I.472, B:D.473, A:D.27 Water bridges: B:D.440, B:S.442, A:Y.28, A:Y.28 Salt bridges: A:H.113, A:H.114 TDL.6: 26 residues within 4Å: Chain C: Y.290, T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, D.473 Chain D: A.25, G.26, D.27, E.50, T.72, V.75, H.114 Ligands: MG.5 31 PLIP interactions: 6 interactions with chain D, 25 interactions with chain C Hydrophobic interactions: D:T.72, C:T.388, C:I.415, C:L.445, C:Y.470, C:I.472, C:I.472 Hydrogen bonds: D:D.27, C:Y.290, C:D.390, C:G.413, C:G.413, C:I.415, C:G.439, C:G.439, C:G.441, C:S.442, C:N.467, C:T.471, C:T.471, C:I.472, C:D.473 Water bridges: D:Y.28, D:Y.28, D:E.50, C:S.391, C:D.440, C:D.440, C:S.442, C:S.442 Salt bridges: D:H.114 TDL.8: 26 residues within 4Å: Chain C: A.25, G.26, D.27, E.50, T.72, V.75, H.114 Chain D: Y.290, T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, L.445, N.467, G.469, Y.470, T.471, I.472, D.473 Ligands: MG.7 29 PLIP interactions: 24 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:T.388, D:I.415, D:L.445, D:Y.470, D:I.472, D:I.472 Hydrogen bonds: D:Y.290, D:D.390, D:G.413, D:G.413, D:I.415, D:G.439, D:D.440, D:G.441, D:S.442, D:N.467, D:T.471, D:T.471, D:I.472, D:D.473, C:D.27 Water bridges: D:S.391, D:D.440, D:S.442, D:S.442, C:Y.28, C:Y.28, C:E.50 Salt bridges: C:H.114

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain D: A.61, R.62, G.65, L.92, P.93, R.221 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.62 Water bridges: D:R.62, D:A.63, D:K.159, D:R.221 GOL.10: 3 residues within 4Å: Chain D: A.368, E.369, R.372 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, D. et al., Double duty for a conserved glutamate in pyruvate decarboxylase: evidence of the participation in stereoelectronically controlled decarboxylation and in protonation of the nascent carbanion/enamine intermediate . Biochemistry (2010)

Release Date

2010-09-08

Peptides

Pyruvate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate decarboxylase