SMTL ID : 2vk1.2 (1 other biounit)

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 23 residues within 4Å: Chain A: G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Chain B: P.26, G.27, E.51, V.76, H.115 Ligands: MG.2, PYR.3 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.415, A:I.415, A:L.449, A:Y.474, A:I.476, A:E.477 Hydrogen bonds: A:T.390, A:G.413, A:I.415, A:G.443, A:G.445, A:S.446, A:N.471, A:N.471, A:T.475, A:I.476 Water bridges: A:S.391, A:D.444, A:S.446, A:S.446, B:E.51 TPP.5: 23 residues within 4Å: Chain A: P.26, G.27, E.51, V.76, H.115 Chain B: G.389, T.390, G.413, S.414, I.415, G.443, D.444, G.445, S.446, L.449, N.471, G.473, Y.474, T.475, I.476, E.477 Ligands: MG.6, PYR.7 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.415, B:I.415, B:L.449, B:Y.474, B:I.476, B:E.477 Hydrogen bonds: B:T.390, B:G.413, B:I.415, B:G.443, B:G.445, B:S.446, B:N.471, B:N.471, B:T.475, B:I.476 Water bridges: B:S.391, B:D.444, B:S.446, B:S.446, A:E.51

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.444, G.445, N.471, G.473 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.444, A:G.473, H2O.16 MG.6: 5 residues within 4Å: Chain B: D.444, G.445, N.471, G.473 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.444, B:G.473, H2O.29

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 7 residues within 4Å: Chain A: G.413, E.477 Chain B: G.27, A.28, H.114, H.115 Ligands: TPP.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.28, A:E.477 Salt bridges: B:H.114, B:H.115 PYR.4: 7 residues within 4Å: Chain A: H.92, C.221, H.225, G.286, A.287, H.310, S.311 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.311 Salt bridges: A:H.92, A:H.225, A:H.310 PYR.7: 8 residues within 4Å: Chain A: G.27, A.28, H.114, H.115 Chain B: G.413, I.476, E.477 Ligands: TPP.5 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.476 Hydrogen bonds: B:E.477, A:A.28 Salt bridges: A:H.114, A:H.115 PYR.8: 7 residues within 4Å: Chain B: H.92, C.221, H.225, G.286, A.287, H.310, S.311 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.311 Salt bridges: B:H.92, B:H.225, B:H.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kutter, S. et al., Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation. J.Biol.Chem. (2009)

Release Date

2009-01-27

Peptides

PYRUVATE DECARBOXYLASE ISOZYME 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

PYRUVATE DECARBOXYLASE ISOZYME 1

Related Entries With Identical Sequence