SMTL ID : 3eya.3 (2 other biounits)

Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 28 residues within 4Å: Chain A: V.380, G.381, T.382, P.383, G.406, S.407, M.408, G.432, D.433, G.434, G.435, M.438, N.460, V.462, L.463, G.464, F.465 Chain B: V.24, T.25, G.26, E.50, S.73, P.76, G.77, H.80, Q.113 Ligands: MG.3, PO4.9 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:V.24, B:P.76, A:L.463 Hydrogen bonds: B:S.73, B:Q.113, A:T.382, A:G.406, A:M.408, A:D.433, A:G.434, A:G.435, A:N.460, A:G.464, A:F.465 Water bridges: B:G.77, B:G.77 TPP.6: 27 residues within 4Å: Chain A: T.25, G.26, E.50, S.73, P.76, G.77, H.80, Q.113 Chain B: V.380, G.381, T.382, P.383, G.406, S.407, M.408, G.432, D.433, G.434, G.435, M.438, N.460, V.462, L.463, G.464, F.465 Ligands: PO4.5, MG.8 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:M.408, B:L.463, A:P.76 Hydrogen bonds: B:T.382, B:G.406, B:M.408, B:D.433, B:G.434, B:G.435, B:N.460, B:G.464, B:F.465, A:S.73, A:Q.113 Water bridges: A:E.50, A:G.77, A:G.77 TPP.10: 28 residues within 4Å: Chain C: V.380, G.381, T.382, P.383, G.406, S.407, M.408, G.432, D.433, G.434, G.435, M.438, N.460, V.462, L.463, G.464, F.465 Chain D: V.24, T.25, G.26, E.50, S.73, P.76, G.77, H.80, Q.113 Ligands: MG.12, PO4.19 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:L.463, D:V.24, D:P.76 Hydrogen bonds: C:T.382, C:G.406, C:M.408, C:D.433, C:G.434, C:G.435, C:N.460, C:G.464, C:F.465, D:S.73, D:Q.113 Water bridges: D:G.77 TPP.14: 26 residues within 4Å: Chain C: T.25, G.26, E.50, S.73, P.76, G.77, H.80, Q.113 Chain D: V.380, G.381, T.382, P.383, G.406, M.408, G.432, D.433, G.434, G.435, M.438, N.460, V.462, L.463, G.464, F.465 Ligands: PO4.13, MG.16 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.463, C:P.76 Hydrogen bonds: D:T.382, D:G.406, D:M.408, D:D.433, D:D.433, D:G.434, D:G.435, D:N.460, D:G.464, D:F.465, C:S.73, C:Q.113

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

FAD.2: 34 residues within 4Å: Chain A: H.92, R.152, G.209, S.210, G.211, A.233, L.234, R.235, G.236, T.251, G.252, L.253, I.254, G.255, G.273, T.274, Q.275, F.276, P.277, Y.278, D.292, I.293, N.294, S.297, G.310, D.311, I.312, V.380, T.384, S.402, F.403, N.404, F.465 Chain B: F.112 34 PLIP interactions: 33 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.234, A:V.380, A:T.384, A:F.465, B:F.112 Hydrogen bonds: A:R.152, A:S.210, A:S.210, A:G.211, A:L.234, A:R.235, A:T.251, A:I.254, A:G.255, A:T.274, A:T.274, A:Q.275, A:Q.275, A:F.276, A:Y.278, A:Y.278, A:I.293, A:S.297, A:D.311, A:D.311, A:I.312, A:F.403, A:N.404 Water bridges: A:H.92, A:L.253, A:N.294 Salt bridges: A:H.92, A:R.235 pi-Stacking: A:Y.278 FAD.7: 31 residues within 4Å: Chain A: F.112 Chain B: H.92, G.209, S.210, G.211, A.233, L.234, R.235, G.236, T.251, G.252, L.253, I.254, G.255, G.273, T.274, Q.275, F.276, P.277, Y.278, D.292, I.293, N.294, S.297, G.310, D.311, I.312, V.380, T.384, F.403, N.404 34 PLIP interactions: 33 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.380, B:T.384, A:F.112 Hydrogen bonds: B:S.210, B:G.211, B:L.234, B:R.235, B:T.251, B:I.254, B:G.255, B:T.274, B:T.274, B:T.274, B:Q.275, B:F.276, B:Y.278, B:I.293, B:N.294, B:S.297, B:D.311, B:I.312, B:F.403, B:N.404 Water bridges: B:T.251, B:L.253, B:L.253, B:L.253, B:L.253, B:Q.275, B:Y.278, B:N.294 Salt bridges: B:H.92, B:R.235 pi-Stacking: B:Y.278 FAD.11: 31 residues within 4Å: Chain C: H.92, G.209, S.210, G.211, A.233, L.234, R.235, G.236, T.251, G.252, L.253, I.254, G.273, T.274, Q.275, F.276, P.277, Y.278, D.292, I.293, N.294, S.297, G.310, D.311, I.312, V.380, T.384, S.402, F.403, N.404 Chain D: F.112 25 PLIP interactions: 24 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.380, C:T.384, D:F.112 Hydrogen bonds: C:S.210, C:G.211, C:L.234, C:R.235, C:T.251, C:I.254, C:G.255, C:T.274, C:T.274, C:Q.275, C:F.276, C:Y.278, C:I.293, C:S.297, C:D.311, C:I.312, C:F.403, C:N.404 Water bridges: C:L.253 Salt bridges: C:H.92, C:R.235 pi-Stacking: C:Y.278 FAD.15: 31 residues within 4Å: Chain C: F.112 Chain D: H.92, G.209, S.210, G.211, A.233, L.234, R.235, G.236, T.251, G.252, L.253, I.254, G.273, T.274, Q.275, F.276, P.277, Y.278, D.292, I.293, N.294, S.297, G.310, D.311, I.312, V.380, T.384, S.402, F.403, N.404 30 PLIP interactions: 29 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.380, D:T.384, C:F.112 Hydrogen bonds: D:S.210, D:G.211, D:L.234, D:R.235, D:T.251, D:I.254, D:G.255, D:T.274, D:T.274, D:T.274, D:Q.275, D:Q.275, D:F.276, D:Y.278, D:Y.278, D:I.293, D:S.297, D:D.311, D:D.311, D:I.312, D:F.403, D:N.404 Water bridges: D:T.251, D:K.313 Salt bridges: D:H.92, D:R.235 pi-Stacking: D:Y.278

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.433, N.460, V.462 Ligands: TPP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.433, A:V.462 MG.8: 4 residues within 4Å: Chain B: D.433, N.460, V.462 Ligands: TPP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.433, B:V.462 MG.12: 5 residues within 4Å: Chain C: D.433, N.460, V.462, G.464 Ligands: TPP.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.433, C:V.462 MG.16: 5 residues within 4Å: Chain D: D.433, N.460, V.462, G.464 Ligands: TPP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.433, D:V.462

9 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: T.173, M.174, H.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.174, A:H.175 PO4.5: 7 residues within 4Å: Chain A: G.26, D.27, S.28, S.73, C.74, Q.113 Ligands: TPP.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.27, A:S.28, A:Q.113, A:Q.113 PO4.9: 7 residues within 4Å: Chain B: G.26, D.27, S.28, S.73, C.74, Q.113 Ligands: TPP.1 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.27, B:S.28, B:S.73, B:Q.113 Water bridges: B:S.73, B:C.74 PO4.13: 6 residues within 4Å: Chain C: G.26, D.27, S.28, S.73, Q.113 Ligands: TPP.14 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.27, C:S.28, C:S.28, C:Q.113, C:Q.113 PO4.17: 4 residues within 4Å: Chain D: E.238, H.239, G.395, R.398 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.395 Water bridges: D:G.395 Salt bridges: D:H.239, D:R.398 PO4.18: 5 residues within 4Å: Chain D: S.367, H.368, D.372, K.392, R.397 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.372 Salt bridges: D:R.397 PO4.19: 7 residues within 4Å: Chain D: G.26, D.27, S.28, S.73, C.74, Q.113 Ligands: TPP.10 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.27, D:S.28, D:S.73, D:S.73, D:Q.113 PO4.20: 2 residues within 4Å: Chain D: E.324, E.325 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.324, D:E.325 PO4.21: 5 residues within 4Å: Chain D: G.252, G.255, F.256, S.257, F.260 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neumann, P. et al., Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-11-04

Peptides

Pyruvate dehydrogenase [cytochrome]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

Pyruvate dehydrogenase [cytochrome]

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