SMTL ID : 3ey9.1

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 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 24 residues within 4Å: Chain A: V.380, G.381, T.382, P.383, G.406, M.408, G.432, D.433, G.434, G.435, N.460, V.462, L.463, G.464 Chain B: T.25, G.26, E.50, S.73, P.76, G.77, H.80, Q.113 Ligands: MG.4, SO4.8 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.463, B:P.76 Hydrogen bonds: A:T.382, A:G.406, A:M.408, A:D.433, A:D.433, A:G.434, A:G.435, A:N.460, A:G.464, B:S.73, B:Q.113 TPP.5: 25 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, M.408, G.432, D.433, G.434, G.435, M.438, N.460, V.462, L.463, G.464 Ligands: SO4.3, MG.7 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.463 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, A:S.73, A:Q.113 TPP.9: 24 residues within 4Å: Chain C: V.380, G.381, T.382, P.383, G.406, M.408, G.432, D.433, G.434, G.435, N.460, V.462, L.463, G.464 Chain D: T.25, G.26, E.50, S.73, P.76, G.77, H.80, Q.113 Ligands: MG.12, SO4.16 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.463, 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, D:S.73, D:Q.113 TPP.13: 25 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 Ligands: SO4.11, MG.15 12 PLIP interactions: 2 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:S.73, C:Q.113, 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 Hydrophobic interactions: D:L.463

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

FAD.2: 33 residues within 4Å: Chain A: 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, S.402, F.403, N.404, Y.549 Chain B: F.112 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.234, A:I.254, A:V.380, A:T.384, A:Y.549, B:F.112 Hydrogen bonds: 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:I.293, A:N.294, A:S.297, A:D.311, A:I.312, A:F.403, A:N.404 Salt bridges: A:H.92, A:R.235 pi-Stacking: A:Y.278 FAD.6: 33 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, S.402, F.403, N.404, Y.549 30 PLIP interactions: 29 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.254, B:V.380, B:T.384, B:Y.549, A:F.112 Hydrogen bonds: B:S.210, 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:Q.275, B:F.276, B:Y.278, B:Y.278, B:I.293, B:N.294, B:S.297, B:D.311, B:D.311, B:I.312, B:F.403, B:N.404 Salt bridges: B:H.92, B:R.235 pi-Stacking: B:Y.278 FAD.10: 33 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.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, Y.549 Chain D: F.112 31 PLIP interactions: 1 interactions with chain D, 30 interactions with chain C Hydrophobic interactions: D:F.112, C:L.234, C:I.254, C:V.380, C:T.384, C:Y.549 Hydrogen bonds: C:S.210, 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:Q.275, C:Q.275, C:F.276, C:Y.278, C:Y.278, C:I.293, C:N.294, C:S.297, C:D.311, C:D.311, C:I.312, C:F.403, C:N.404 Salt bridges: C:H.92, C:R.235 pi-Stacking: C:Y.278 FAD.14: 33 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.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, Y.549 29 PLIP interactions: 28 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:I.254, D:V.380, D:T.384, D:Y.549, C:F.112 Hydrogen bonds: D:S.210, 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:F.276, D:Y.278, D:I.293, D:N.294, D:S.297, D:D.311, D:I.312, D:F.403, D:N.404 Salt bridges: D:H.92, D:R.235 pi-Stacking: D:Y.278

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 7 residues within 4Å: Chain A: G.26, D.27, S.28, S.73, C.74, Q.113 Ligands: TPP.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.27, A:S.28, A:S.73, A:Q.113, A:Q.113 SO4.8: 7 residues within 4Å: Chain B: G.26, D.27, S.28, S.73, C.74, Q.113 Ligands: TPP.1 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.27, B:S.28, B:S.73, B:S.73, B:Q.113 SO4.11: 7 residues within 4Å: Chain C: G.26, D.27, S.28, S.73, C.74, Q.113 Ligands: TPP.13 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.27, C:S.28, C:S.73, C:Q.113, C:Q.113 SO4.16: 7 residues within 4Å: Chain D: G.26, D.27, S.28, S.73, C.74, Q.113 Ligands: TPP.9 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: G.432, D.433, F.458, N.460, V.462 Ligands: TPP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.433 MG.7: 6 residues within 4Å: Chain B: G.432, D.433, F.458, N.460, V.462 Ligands: TPP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.433 MG.12: 6 residues within 4Å: Chain C: G.432, D.433, F.458, N.460, V.462 Ligands: TPP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.433 MG.15: 6 residues within 4Å: Chain D: G.432, D.433, F.458, N.460, V.462 Ligands: TPP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.433

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
A

B
B

C
A

D
B

Pyruvate dehydrogenase [cytochrome]