SMTL ID : 6u0p.1

Crystal structure of PieE, the flavin-dependent monooxygenase involved in the biosynthesis of piericidin A1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-hexamer

Ligands

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

FAD.1: 27 residues within 4Å: Chain A: V.21, G.22, G.23, G.24, P.25, A.26, V.44, N.45, R.46, H.47, R.55, A.56, Q.129, H.152, E.153, F.154, A.187, D.188, G.189, W.299, G.318, D.319, P.326, G.329, G.331, L.332 Ligands: GOL.7 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:R.55 Hydrogen bonds: A:G.23, A:G.24, A:A.26, A:N.45, A:R.46, A:H.47, A:H.47, A:R.55, A:Q.129, A:Q.129, A:F.154, A:F.154, A:D.319, A:D.319 Water bridges: A:G.23, A:G.27, A:H.57, A:H.57, A:H.57, A:L.58, A:E.133, A:G.189, A:A.190, A:A.320, A:P.326 Salt bridges: A:R.55 pi-Stacking: A:W.299, A:W.299, A:W.299 pi-Cation interactions: A:R.46 FAD.9: 29 residues within 4Å: Chain B: V.21, G.22, G.23, G.24, P.25, A.26, V.44, N.45, R.46, H.47, R.55, A.56, Q.129, H.152, E.153, F.154, A.187, D.188, G.189, R.193, W.299, G.318, D.319, P.326, G.329, G.331, L.332, A.335 Ligands: GOL.15 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:R.55, B:W.299, B:W.299 Hydrogen bonds: B:G.23, B:G.24, B:A.26, B:N.45, B:R.46, B:R.46, B:H.47, B:H.47, B:R.55, B:R.55, B:Q.129, B:Q.129, B:F.154, B:F.154, B:R.193, B:D.319, B:D.319 Water bridges: B:H.57, B:H.57, B:H.57, B:E.133, B:G.189, B:A.190, B:G.318, B:D.319, B:A.320, B:P.326 Salt bridges: B:R.55 pi-Stacking: B:W.299, B:W.299 FAD.18: 26 residues within 4Å: Chain C: V.21, G.22, G.23, G.24, P.25, A.26, V.44, N.45, R.46, H.47, R.55, A.56, Q.129, H.152, E.153, F.154, A.187, D.188, G.189, W.299, G.318, D.319, P.326, G.331, L.332 Ligands: GOL.24 35 PLIP interactions: 35 interactions with chain C Hydrophobic interactions: C:R.55 Hydrogen bonds: C:G.23, C:G.24, C:A.26, C:N.45, C:R.46, C:R.46, C:H.47, C:H.47, C:R.55, C:Q.129, C:Q.129, C:F.154, C:F.154, C:D.319, C:D.319 Water bridges: C:G.23, C:G.27, C:R.55, C:H.57, C:H.57, C:E.133, C:E.133, C:G.189, C:A.190, C:A.190, C:G.318, C:A.320, C:P.326, C:A.335 Salt bridges: C:R.55 pi-Stacking: C:W.299, C:W.299, C:W.299 pi-Cation interactions: C:R.55 FAD.26: 26 residues within 4Å: Chain D: V.21, G.22, G.23, G.24, P.25, A.26, V.44, N.45, R.46, H.47, R.55, A.56, Q.129, H.152, E.153, F.154, A.187, D.188, G.189, R.193, W.299, G.318, D.319, P.326, G.331, L.332 35 PLIP interactions: 35 interactions with chain D Hydrophobic interactions: D:R.55, D:W.299 Hydrogen bonds: D:G.23, D:G.24, D:A.26, D:N.45, D:R.46, D:H.47, D:H.47, D:R.55, D:Q.129, D:Q.129, D:F.154, D:F.154, D:R.193, D:D.319 Water bridges: D:G.23, D:G.27, D:R.55, D:H.57, D:H.57, D:H.57, D:L.58, D:E.133, D:A.190, D:D.319, D:A.320, D:A.320, D:P.326, D:A.335 Salt bridges: D:R.55 pi-Stacking: D:W.299, D:W.299, D:W.299 pi-Cation interactions: D:R.46 FAD.36: 28 residues within 4Å: Chain E: V.21, G.22, G.23, G.24, P.25, A.26, V.44, N.45, R.46, H.47, R.55, A.56, Q.129, H.152, E.153, F.154, A.187, D.188, G.189, R.193, W.299, G.318, D.319, P.326, G.329, G.331, L.332 Ligands: GOL.42 40 PLIP interactions: 40 interactions with chain E Hydrophobic interactions: E:R.55, E:W.299, E:W.299 Hydrogen bonds: E:G.23, E:G.24, E:A.26, E:N.45, E:R.46, E:H.47, E:H.47, E:R.55, E:A.56, E:Q.129, E:Q.129, E:F.154, E:F.154, E:D.319, E:D.319 Water bridges: E:G.23, E:G.27, E:R.55, E:R.55, E:R.55, E:R.55, E:R.55, E:H.57, E:H.57, E:H.57, E:E.133, E:A.190, E:D.319, E:A.320, E:A.320, E:P.326, E:L.330, E:G.331, E:G.331 Salt bridges: E:R.55 pi-Stacking: E:W.299, E:W.299 FAD.46: 25 residues within 4Å: Chain F: V.21, G.22, G.23, G.24, P.25, A.26, V.44, N.45, R.46, H.47, R.55, A.56, Q.129, H.152, E.153, F.154, A.187, D.188, G.189, W.299, G.318, D.319, P.326, G.331, L.332 34 PLIP interactions: 34 interactions with chain F Hydrophobic interactions: F:R.55, F:W.299 Hydrogen bonds: F:G.23, F:A.26, F:N.45, F:R.46, F:H.47, F:R.55, F:Q.129, F:Q.129, F:F.154, F:F.154, F:D.319, F:D.319 Water bridges: F:G.23, F:G.24, F:G.24, F:H.57, F:H.57, F:H.57, F:H.57, F:L.58, F:E.133, F:G.189, F:A.190, F:A.320, F:P.326, F:L.330, F:A.335 Salt bridges: F:R.55 pi-Stacking: F:W.299, F:W.299, F:W.299 pi-Cation interactions: F:R.55

12 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 10 residues within 4Å: Chain A: I.14, H.41, V.145, G.146, Q.147, R.149 Chain F: L.530, G.535, G.537, P.538 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:G.535, A:Q.147, A:R.149 Water bridges: F:N.485 PGE.3: 8 residues within 4Å: Chain A: G.234, P.241, A.242, G.244, F.261, L.384, I.385, P.388 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.234 Water bridges: A:I.385 PGE.10: 8 residues within 4Å: Chain B: H.41, V.145, G.146, Q.147, R.149 Chain C: L.530, G.535, G.537 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Water bridges: C:R.513, C:R.513 Hydrogen bonds: B:Q.147, B:R.149 PGE.11: 10 residues within 4Å: Chain B: F.91, M.92, M.233, G.234, A.235, P.241, G.244, L.384, I.387, P.388 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.92, B:M.92 Water bridges: B:I.385 PGE.19: 9 residues within 4Å: Chain B: L.530, G.537, P.538 Chain C: I.14, V.16, H.41, V.145, G.146, Q.147 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.147 Water bridges: B:N.485, B:R.513 PGE.20: 11 residues within 4Å: Chain C: F.91, M.92, M.233, G.234, A.235, P.241, G.244, F.261, L.384, I.387, P.388 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:M.92, C:M.92 PGE.27: 7 residues within 4Å: Chain D: V.16, H.41, V.145, G.146, Q.147 Chain E: L.530, G.537 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:Q.147, E:G.535 Water bridges: E:R.513 PGE.28: 10 residues within 4Å: Chain D: M.233, G.234, A.235, P.241, G.244, F.261, M.381, L.384, I.385, P.388 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.234 PGE.37: 8 residues within 4Å: Chain D: R.513, L.530, G.535 Chain E: I.14, H.41, V.145, G.146, Q.147 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Water bridges: D:N.485, D:R.513, D:R.513 Hydrogen bonds: E:G.146, E:Q.147 PGE.38: 12 residues within 4Å: Chain E: F.91, M.92, M.233, G.234, A.235, P.241, A.242, G.244, L.384, I.385, I.387, P.388 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:M.92, E:M.92, E:G.244 Water bridges: E:A.242, E:I.385 PGE.47: 9 residues within 4Å: Chain A: L.530, G.537, P.538 Chain F: I.14, H.41, C.144, V.145, G.146, Q.147 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Q.147 PGE.48: 12 residues within 4Å: Chain F: F.91, M.92, M.233, G.234, A.235, P.241, A.242, G.244, L.384, I.385, I.387, P.388 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:M.92 Water bridges: F:M.381

6 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 10 residues within 4Å: Chain A: G.64, F.67, A.73, V.76, E.77, R.117, P.121, S.122, G.123, C.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.123 Water bridges: A:G.64 1PE.12: 10 residues within 4Å: Chain B: G.64, F.67, A.73, V.76, E.77, R.117, P.121, S.122, G.123, C.125 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.123 Water bridges: B:G.64, B:R.117, B:C.125 1PE.21: 10 residues within 4Å: Chain C: G.64, F.67, A.73, V.76, E.77, R.117, P.121, S.122, G.123, C.125 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.117, C:G.123 Water bridges: C:G.64 1PE.29: 9 residues within 4Å: Chain D: G.64, F.67, V.76, E.77, R.117, P.121, S.122, G.123, C.125 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.123 Water bridges: D:R.117, D:S.122, D:S.122 1PE.39: 10 residues within 4Å: Chain E: G.64, F.67, A.73, V.76, E.77, R.117, P.121, S.122, G.123, C.125 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:R.117, E:G.123 Water bridges: E:G.64, E:R.68, E:C.125 1PE.49: 10 residues within 4Å: Chain F: G.64, F.67, A.73, V.76, E.77, R.117, P.121, S.122, G.123, C.125 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.123 Water bridges: F:G.64, F:E.77, F:R.117

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: G.71, I.72, A.73, D.74 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: H.47, H.48, R.171 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: G.71, I.72, A.73, D.74 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain C: G.71, I.72, A.73, D.74 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain C: H.47, H.48, R.171 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain D: G.71, I.72, A.73, D.74 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain D: H.47, H.48, R.171 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain E: G.71, I.72, A.73, D.74 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain E: H.47, H.48, R.171 Ligand excluded by PLIP CL.50: 4 residues within 4Å: Chain F: G.71, I.72, A.73, D.74 Ligand excluded by PLIP

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: H.57, M.233, P.326, T.327 Ligands: FAD.1 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: D.460, E.461, R.462, P.464 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain A: Y.542 Chain B: A.87, N.88, G.104, N.108, G.109, P.110 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: H.57, L.231, V.248, L.259, P.326, T.327 Ligands: FAD.9 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: P.110, D.111 Chain B: G.114, E.115 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: R.222 Chain B: R.487 Chain C: Q.141, F.150 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: H.57, L.259, P.326, T.327 Ligands: FAD.18 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain C: P.110, D.111 Chain D: G.114, E.115, A.118 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain D: H.57, V.248, P.326, T.327 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: Q.141, F.150 Chain E: R.487 Chain F: R.222 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain C: Y.542 Chain D: A.87, N.88, G.104, N.108, G.109, P.110 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain C: R.222 Chain D: R.487 Chain E: H.48, G.49, T.50, F.150 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain E: H.57, L.231, V.248, P.326, T.327 Ligands: FAD.36 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain E: A.87, N.88, G.104, N.108, G.109, P.110 Chain F: Y.542 Ligand excluded by PLIP GOL.44: 5 residues within 4Å: Chain E: P.110, D.111 Chain F: G.114, E.115, A.118 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain E: G.114, E.115, A.118 Chain F: P.110, D.111 Ligand excluded by PLIP GOL.51: 4 residues within 4Å: Chain F: M.233, F.261, P.326, T.327 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manenda, M.S. et al., Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. J.Biol.Chem. (2020)

Release Date

2020-03-11

Peptides

2,4-dichlorophenol 6-monooxygenase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

2,4-dichlorophenol 6-monooxygenase

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