SMTL ID : 1v5g.1

Crystal Structure of the Reaction Intermediate between Pyruvate oxidase containing FAD and TPP, and Substrate Pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.439, N.466, E.468 Ligands: HTL.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.439, A:E.468, H2O.1 MG.4: 4 residues within 4Å: Chain B: D.439, N.466, E.468 Ligands: HTL.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.439, B:E.468, H2O.27 MG.7: 4 residues within 4Å: Chain C: D.439, N.466, E.468 Ligands: HTL.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.439, C:E.468, H2O.54 MG.10: 4 residues within 4Å: Chain D: D.439, N.466, E.468 Ligands: HTL.12 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.439, D:E.468, H2O.80

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.2: 30 residues within 4Å: Chain A: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, V.386, S.408, P.409, A.412, F.471 Chain B: F.113 Ligands: HTL.3 27 PLIP interactions: 25 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.257, A:V.386, A:A.412, A:F.471, B:F.113, B:F.113 Hydrogen bonds: A:I.213, A:G.214, A:T.236, A:T.236, A:G.237, A:T.254, A:V.257, A:S.277, A:N.278, A:I.299, A:D.317, A:A.318, A:P.409 Water bridges: A:N.278, A:N.278, A:N.278, A:N.278, A:D.300, A:D.300 Salt bridges: A:K.238, A:K.238 FAD.5: 30 residues within 4Å: Chain A: F.113 Chain B: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, V.386, S.408, P.409, A.412, F.471 Ligands: HTL.6 27 PLIP interactions: 25 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.257, B:V.386, B:A.412, B:F.471, A:F.113, A:F.113 Hydrogen bonds: B:I.213, B:G.214, B:T.236, B:T.236, B:G.237, B:T.254, B:V.257, B:S.277, B:N.278, B:I.299, B:D.317, B:A.318, B:P.409 Water bridges: B:N.278, B:N.278, B:N.278, B:N.278, B:D.300, B:D.300 Salt bridges: B:K.238, B:K.238 FAD.8: 30 residues within 4Å: Chain C: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, V.386, S.408, P.409, A.412, F.471 Chain D: F.113 Ligands: HTL.9 27 PLIP interactions: 25 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.257, C:V.386, C:A.412, C:F.471, D:F.113, D:F.113 Hydrogen bonds: C:I.213, C:G.214, C:T.236, C:G.237, C:T.254, C:V.257, C:S.277, C:N.278, C:I.299, C:D.317, C:D.317, C:A.318, C:P.409 Water bridges: C:Y.210, C:N.278, C:N.278, C:N.278, C:N.278, C:D.300 Salt bridges: C:K.238, C:K.238 FAD.11: 30 residues within 4Å: Chain C: F.113 Chain D: G.212, I.213, G.214, T.236, G.237, K.238, T.254, Y.255, R.256, V.257, G.276, S.277, N.278, F.279, P.280, F.281, D.298, I.299, D.300, M.303, G.316, D.317, A.318, V.386, S.408, P.409, A.412, F.471 Ligands: HTL.12 27 PLIP interactions: 25 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:V.257, D:V.386, D:A.412, D:F.471, C:F.113, C:F.113 Hydrogen bonds: D:I.213, D:G.214, D:T.236, D:G.237, D:T.254, D:V.257, D:S.277, D:N.278, D:I.299, D:D.317, D:D.317, D:A.318, D:P.409 Water bridges: D:Y.210, D:N.278, D:N.278, D:N.278, D:N.278, D:D.300 Salt bridges: D:K.238, D:K.238

4 x HTL: 2-ACETYL-THIAMINE DIPHOSPHATE(Non-covalent)

HTL.3: 26 residues within 4Å: Chain A: V.386, G.387, N.388, S.389, A.412, M.414, G.438, D.439, G.440, A.441, M.444, N.466, E.468, Y.469, A.470, F.471, I.472 Chain B: P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Ligands: MG.1, FAD.2 23 PLIP interactions: 3 interactions with chain B, 20 interactions with chain A Hydrophobic interactions: B:P.77, A:V.386, A:Y.469, A:F.471, A:F.471, A:I.472 Hydrogen bonds: B:S.74, B:Q.114, A:V.386, A:N.388, A:S.389, A:A.412, A:M.414, A:G.440, A:A.441, A:N.466, A:E.468, A:A.470, A:F.471 Water bridges: A:G.438, A:G.438, A:D.439, A:D.439 HTL.6: 26 residues within 4Å: Chain A: P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Chain B: V.386, G.387, N.388, S.389, A.412, M.414, G.438, D.439, G.440, A.441, M.444, N.466, E.468, Y.469, A.470, F.471, I.472 Ligands: MG.4, FAD.5 23 PLIP interactions: 20 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.386, B:Y.469, B:F.471, B:F.471, B:I.472, A:P.77 Hydrogen bonds: B:V.386, B:N.388, B:S.389, B:A.412, B:M.414, B:G.440, B:A.441, B:N.466, B:E.468, B:A.470, B:F.471, A:S.74, A:Q.114 Water bridges: B:G.438, B:G.438, B:D.439, B:D.439 HTL.9: 26 residues within 4Å: Chain C: V.386, G.387, N.388, S.389, A.412, M.414, G.438, D.439, G.440, A.441, M.444, N.466, E.468, Y.469, A.470, F.471, I.472 Chain D: P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Ligands: MG.7, FAD.8 23 PLIP interactions: 20 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.386, C:Y.469, C:F.471, C:F.471, C:I.472, D:P.77 Hydrogen bonds: C:V.386, C:N.388, C:S.389, C:A.412, C:M.414, C:G.440, C:A.441, C:N.466, C:E.468, C:A.470, C:F.471, D:S.74, D:Q.114 Water bridges: C:G.438, C:G.438, C:D.439, C:D.439 HTL.12: 26 residues within 4Å: Chain C: P.25, E.51, S.74, P.77, G.78, H.81, Q.114 Chain D: V.386, G.387, N.388, S.389, A.412, M.414, G.438, D.439, G.440, A.441, M.444, N.466, E.468, Y.469, A.470, F.471, I.472 Ligands: MG.10, FAD.11 23 PLIP interactions: 20 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:V.386, D:Y.469, D:F.471, D:F.471, D:I.472, C:P.77 Hydrogen bonds: D:V.386, D:N.388, D:S.389, D:A.412, D:M.414, D:G.440, D:A.441, D:N.466, D:E.468, D:A.470, D:F.471, C:S.74, C:Q.114 Water bridges: D:G.438, D:G.438, D:D.439, D:D.439

Links

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Citation

Juan, E.C. et al., The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis. Acta Crystallogr.,Sect.F (2007)

Release Date

2005-06-28

Peptides

Pyruvate oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Pyruvate oxidase

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