SMTL ID : 5o8r.1

The crystal structure of DfoA bound to FAD and NADP; the desferrioxamine biosynthetic pathway cadaverine monooxygenase from the fire blight disease pathogen Erwinia amylovora

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 25 residues within 4Å: Chain A: G.15, G.17, P.18, F.19, D.39, Q.40, N.41, W.46, H.47, L.57, Q.58, T.59, T.121, R.122, V.123, G.158, T.159, G.160, P.161, F.349, N.383, P.394, D.395, L.396 Ligands: NAP.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.46, A:W.46, A:H.47 Hydrogen bonds: A:F.19, A:Q.40, A:N.41, A:Q.58, A:V.123, A:V.123, A:N.383, A:P.394, A:P.394, A:L.396 Water bridges: A:I.16, A:G.17, A:N.20 FAD.3: 25 residues within 4Å: Chain B: G.15, G.17, P.18, F.19, D.39, Q.40, N.41, W.46, H.47, L.57, Q.58, T.59, T.121, R.122, V.123, G.158, T.159, G.160, P.161, F.349, N.383, P.394, D.395, L.396 Ligands: NAP.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.46, B:W.46, B:H.47 Hydrogen bonds: B:F.19, B:Q.40, B:N.41, B:Q.58, B:V.123, B:V.123, B:N.383, B:P.394, B:P.394, B:L.396 Water bridges: B:I.16, B:G.17, B:N.20 FAD.5: 28 residues within 4Å: Chain C: G.15, I.16, G.17, P.18, F.19, D.39, Q.40, N.41, W.46, H.47, M.50, L.57, Q.58, R.100, T.121, R.122, V.123, G.158, T.159, G.160, P.161, Y.342, F.349, N.383, P.394, D.395, L.396 Ligands: NAP.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.342 Hydrogen bonds: C:I.16, C:F.19, C:Q.40, C:Q.58, C:V.123, C:V.123, C:N.383, C:P.394, C:D.395, C:L.396 Water bridges: C:G.17, C:N.20 FAD.7: 28 residues within 4Å: Chain D: G.15, I.16, G.17, P.18, F.19, D.39, Q.40, N.41, W.46, H.47, M.50, L.57, Q.58, R.100, T.121, R.122, V.123, G.158, T.159, G.160, P.161, Y.342, F.349, N.383, P.394, D.395, L.396 Ligands: NAP.8 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.342 Hydrogen bonds: D:I.16, D:F.19, D:Q.40, D:Q.58, D:V.123, D:V.123, D:N.383, D:P.394, D:L.396 Water bridges: D:G.17, D:N.20

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 26 residues within 4Å: Chain A: Q.58, R.100, W.164, P.166, L.198, G.199, S.200, G.201, Q.202, S.203, T.226, R.227, A.228, Y.232, K.268, Y.271, K.272, S.303, E.304, L.305, A.339, T.340, G.341, Y.342, P.394 Ligands: FAD.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Q.58 Hydrogen bonds: A:R.100, A:S.200, A:G.201, A:S.203, A:S.203, A:S.203, A:A.204, A:T.226, A:R.227, A:L.305, A:L.305, A:A.339 Water bridges: A:G.341 Salt bridges: A:R.227, A:K.268, A:K.272, A:K.272 pi-Cation interactions: A:R.227 NAP.4: 26 residues within 4Å: Chain B: Q.58, R.100, W.164, P.166, L.198, G.199, S.200, G.201, Q.202, S.203, T.226, R.227, A.228, Y.232, K.268, Y.271, K.272, S.303, E.304, L.305, A.339, T.340, G.341, Y.342, P.394 Ligands: FAD.3 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Q.58 Hydrogen bonds: B:R.100, B:S.200, B:G.201, B:S.203, B:S.203, B:S.203, B:A.204, B:T.226, B:R.227, B:Y.232, B:L.305, B:L.305, B:A.339 Water bridges: B:G.341 Salt bridges: B:R.227, B:K.268, B:K.272, B:K.272 pi-Cation interactions: B:R.227 NAP.6: 28 residues within 4Å: Chain C: H.56, L.57, Q.58, R.100, W.164, L.198, G.199, S.200, G.201, Q.202, S.203, A.204, E.206, T.226, R.227, A.228, Y.232, K.268, Y.271, K.272, S.303, E.304, L.305, A.339, T.340, G.341, Y.342 Ligands: FAD.5 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:Q.202 Hydrogen bonds: C:H.56, C:Q.58, C:R.100, C:S.200, C:G.201, C:S.203, C:S.203, C:A.204, C:T.226, C:R.227, C:A.228, C:Y.232, C:Y.232, C:Y.271, C:L.305, C:L.305 Water bridges: C:S.179, C:G.341 Salt bridges: C:R.227, C:K.268, C:K.272 pi-Cation interactions: C:R.227 NAP.8: 28 residues within 4Å: Chain D: H.56, L.57, Q.58, R.100, W.164, L.198, G.199, S.200, G.201, Q.202, S.203, A.204, E.206, T.226, R.227, A.228, Y.232, K.268, Y.271, K.272, S.303, E.304, L.305, A.339, T.340, G.341, Y.342 Ligands: FAD.7 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:Q.202 Hydrogen bonds: D:H.56, D:Q.58, D:R.100, D:S.200, D:G.201, D:S.203, D:S.203, D:A.204, D:T.226, D:R.227, D:A.228, D:Y.232, D:Y.271, D:L.305, D:L.305 Water bridges: D:S.179, D:G.341 Salt bridges: D:R.227, D:K.268, D:K.272 pi-Cation interactions: D:R.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salomone-Stagni, M. et al., A complete structural characterization of the desferrioxamine E biosynthetic pathway from the fire blight pathogen Erwinia amylovora. J. Struct. Biol. (2018)

Release Date

2018-02-28

Peptides

L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

L-lysine 6-monooxygenase involved in desferrioxamine biosynthesis

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