SMTL ID : 4zp1.1

Crystal structure of Zymomonas mobilis pyruvate decarboxylase variant Glu473Ala

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.440, G.441, N.467, G.469 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.440, A:G.469, H2O.4 MG.4: 4 residues within 4Å: Chain B: D.440, N.467, G.469 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.440, B:G.469, H2O.8 MG.8: 4 residues within 4Å: Chain C: D.440, N.467, G.469 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.440, C:G.469, H2O.14 MG.11: 4 residues within 4Å: Chain D: D.440, N.467, G.469 Ligands: TPP.12 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.440, D:G.469

2 x NI: NICKEL (II) ION(Non-covalent)

NI.2: 3 residues within 4Å: Chain A: H.106, H.122 Chain C: H.122 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:H.122, A:H.122 NI.5: 3 residues within 4Å: Chain B: H.106 Chain D: H.106, H.122 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:H.106, D:H.106, D:H.122, H2O.11

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 21 residues within 4Å: Chain A: 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 Chain B: A.25, G.26, E.50, V.75, H.114 Ligands: MG.1 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.415, A:I.415, A:L.445, A:Y.470, A:Y.470, A:I.472 Hydrogen bonds: A:D.390, A:G.413, A:I.415, A:G.439, A:G.441, A:S.442, A:N.467, A:G.469, A:T.471, A:T.471, A:I.472 Water bridges: A:S.391, A:D.440, A:D.440, A:S.442, A:S.442 TPP.7: 21 residues within 4Å: Chain A: A.25, G.26, E.50, V.75, H.114 Chain B: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, N.467, G.469, Y.470, T.471, I.472 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.415, B:Y.470, B:Y.470, B:I.472 Hydrogen bonds: B:D.390, B:G.413, B:I.415, B:G.439, B:G.441, B:S.442, B:N.467, B:T.471, B:I.472 Water bridges: B:D.440, B:D.440 TPP.10: 20 residues within 4Å: Chain C: G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, N.467, G.469, Y.470, T.471, I.472 Chain D: A.25, G.26, E.50, V.75, H.114 Ligands: MG.8 20 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.415, C:Y.470, C:Y.470, C:I.472 Hydrogen bonds: C:D.390, C:G.413, C:I.415, C:G.439, C:D.440, C:G.441, C:S.442, C:N.467, C:T.471, C:I.472 Water bridges: C:S.391, C:D.440, C:D.440, C:S.442, C:S.442, D:E.50 TPP.12: 21 residues within 4Å: Chain C: A.25, G.26, E.50, V.75, H.114 Chain D: T.388, G.389, D.390, G.413, H.414, I.415, G.439, D.440, G.441, S.442, N.467, G.469, Y.470, T.471, I.472 Ligands: MG.11 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.415, D:I.415, D:Y.470, D:Y.470, D:I.472 Hydrogen bonds: D:D.390, D:G.413, D:I.415, D:G.439, D:G.439, D:D.440, D:G.441, D:S.442, D:T.471, D:T.471, D:I.472 Water bridges: D:S.391

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain B: A.89, E.90, N.91, S.218, A.245, V.286, Y.408, M.410, Q.411 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.89, B:N.91, B:S.218, B:S.218, B:Y.408, B:M.410 GOL.9: 6 residues within 4Å: Chain C: A.63, R.405, Y.425, A.429, E.431, R.432 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.425 Water bridges: C:E.431

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wechsler, C. et al., Tuning and Switching Enantioselectivity of Asymmetric Carboligation in an Enzyme through Mutational Analysis of a Single Hot Spot. Chembiochem (2015)

Release Date

2015-11-04

Peptides

Pyruvate decarboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate decarboxylase