SMTL ID : 4ocg.2 (1 other biounit)

Structure of the Shewanella loihica PV-4 NADH-dependent persulfide reductase F161A Mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-hexamer

Ligands

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

FAD.1: 30 residues within 4Å: Chain A: I.7, G.8, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Chain B: Y.446, A.447, P.448 Ligands: COA.2 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.42, A:L.133, A:I.162 Hydrogen bonds: A:G.9, A:A.11, A:G.12, A:R.34, A:R.34, A:N.42, A:N.42, A:N.42, A:V.81, A:V.81, A:G.114, A:D.303, A:P.319, A:A.321, A:G.322, B:Y.446 Water bridges: A:V.10, A:G.13, A:A.115, A:A.115 Salt bridges: A:R.134 pi-Cation interactions: A:R.34 FAD.3: 32 residues within 4Å: Chain A: Y.446, A.447, P.448 Chain B: I.7, G.8, G.9, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, P.46, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Ligands: COA.4 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.42, B:L.133, B:I.162 Hydrogen bonds: B:G.9, B:A.11, B:G.12, B:R.34, B:R.34, B:N.42, B:N.42, B:N.42, B:V.81, B:V.81, B:S.112, B:G.114, B:D.303, B:P.319, B:A.321, A:Y.446 Water bridges: B:R.134, B:R.134, B:A.304, B:G.322 Salt bridges: B:R.134 pi-Cation interactions: B:R.34 FAD.5: 30 residues within 4Å: Chain C: I.7, G.8, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Chain D: Y.446, A.447, P.448 Ligands: COA.6 25 PLIP interactions: 24 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:N.42, C:L.133, C:I.162 Hydrogen bonds: C:G.9, C:A.11, C:G.12, C:R.34, C:R.34, C:N.42, C:N.42, C:N.42, C:V.81, C:V.81, C:G.114, C:D.303, C:P.319, C:A.321, C:G.322, D:Y.446 Water bridges: C:V.10, C:G.13, C:A.115, C:A.115 Salt bridges: C:R.134 pi-Cation interactions: C:R.34 FAD.7: 32 residues within 4Å: Chain C: Y.446, A.447, P.448 Chain D: I.7, G.8, G.9, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, P.46, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Ligands: COA.8 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:N.42, D:L.133, D:I.162 Hydrogen bonds: D:G.9, D:A.11, D:G.12, D:R.34, D:R.34, D:N.42, D:N.42, D:N.42, D:V.81, D:V.81, D:S.112, D:G.114, D:D.303, D:P.319, D:A.321, C:Y.446 Water bridges: D:R.134, D:R.134, D:A.304, D:G.322 Salt bridges: D:R.134 pi-Cation interactions: D:R.34 FAD.9: 30 residues within 4Å: Chain E: I.7, G.8, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Chain F: Y.446, A.447, P.448 Ligands: COA.10 25 PLIP interactions: 24 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:N.42, E:L.133, E:I.162 Hydrogen bonds: E:G.9, E:A.11, E:G.12, E:R.34, E:R.34, E:N.42, E:N.42, E:N.42, E:V.81, E:V.81, E:G.114, E:D.303, E:P.319, E:A.321, E:G.322, F:Y.446 Water bridges: E:V.10, E:G.13, E:A.115, E:A.115 Salt bridges: E:R.134 pi-Cation interactions: E:R.34 FAD.11: 32 residues within 4Å: Chain E: Y.446, A.447, P.448 Chain F: I.7, G.8, G.9, V.10, A.11, G.12, F.32, E.33, R.34, N.42, C.43, P.46, H.79, E.80, V.81, S.112, P.113, G.114, L.133, R.134, I.162, L.271, G.302, D.303, P.319, L.320, A.321, A.324 Ligands: COA.12 25 PLIP interactions: 24 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:N.42, F:L.133, F:I.162 Hydrogen bonds: F:G.9, F:A.11, F:G.12, F:R.34, F:R.34, F:N.42, F:N.42, F:N.42, F:V.81, F:V.81, F:S.112, F:G.114, F:D.303, F:P.319, F:A.321, E:Y.446 Water bridges: F:R.134, F:R.134, F:A.304, F:G.322 Salt bridges: F:R.134 pi-Cation interactions: F:R.34

6 x COA: COENZYME A(Non-covalent)

COA.2: 32 residues within 4Å: Chain A: V.10, A.11, A.14, S.15, A.18, R.19, R.22, S.39, F.40, N.42, C.43, L.61, Q.62, F.67, F.71, A.321, N.325, R.329 Chain B: V.380, Y.388, Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538, N.553 Ligands: FAD.1 16 PLIP interactions: 7 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:K.454, B:K.454, B:Q.459, B:N.466, B:V.533, A:F.40, A:N.325 Salt bridges: B:K.454, B:K.454, A:R.19, A:R.22, A:R.22, A:R.329 Hydrophobic interactions: A:V.10, A:Q.62, A:F.67 COA.4: 29 residues within 4Å: Chain A: V.380, Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538 Chain B: V.10, A.11, A.14, S.15, A.18, R.19, R.22, S.39, F.40, N.42, C.43, Q.62, F.67, F.71, A.321, N.325, R.329 Ligands: FAD.3 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain A Hydrophobic interactions: B:V.10, B:A.14, B:Q.62, B:F.67 Hydrogen bonds: B:F.40, B:N.325, A:K.454, A:K.454, A:Q.459, A:N.466, A:V.533, A:N.538 Salt bridges: B:R.19, B:R.22, B:R.22, B:R.329, A:K.454, A:K.454 COA.6: 32 residues within 4Å: Chain C: V.10, A.11, A.14, S.15, A.18, R.19, R.22, S.39, F.40, N.42, C.43, L.61, Q.62, F.67, F.71, A.321, N.325, R.329 Chain D: V.380, Y.388, Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538, N.553 Ligands: FAD.5 16 PLIP interactions: 7 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:K.454, D:K.454, D:Q.459, D:N.466, D:V.533, C:F.40, C:N.325 Salt bridges: D:K.454, D:K.454, C:R.19, C:R.22, C:R.22, C:R.329 Hydrophobic interactions: C:V.10, C:Q.62, C:F.67 COA.8: 29 residues within 4Å: Chain C: V.380, Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538 Chain D: V.10, A.11, A.14, S.15, A.18, R.19, R.22, S.39, F.40, N.42, C.43, Q.62, F.67, F.71, A.321, N.325, R.329 Ligands: FAD.7 18 PLIP interactions: 8 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:K.454, C:K.454, C:Q.459, C:N.466, C:V.533, C:N.538, D:F.40, D:N.325 Salt bridges: C:K.454, C:K.454, D:R.19, D:R.22, D:R.22, D:R.329 Hydrophobic interactions: D:V.10, D:A.14, D:Q.62, D:F.67 COA.10: 32 residues within 4Å: Chain E: V.10, A.11, A.14, S.15, A.18, R.19, R.22, S.39, F.40, N.42, C.43, L.61, Q.62, F.67, F.71, A.321, N.325, R.329 Chain F: V.380, Y.388, Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538, N.553 Ligands: FAD.9 16 PLIP interactions: 9 interactions with chain E, 7 interactions with chain F Hydrophobic interactions: E:V.10, E:Q.62, E:F.67 Hydrogen bonds: E:F.40, E:N.325, F:K.454, F:K.454, F:Q.459, F:N.466, F:V.533 Salt bridges: E:R.19, E:R.22, E:R.22, E:R.329, F:K.454, F:K.454 COA.12: 29 residues within 4Å: Chain E: V.380, Y.446, K.454, Q.459, F.462, V.463, N.466, V.533, G.534, L.535, N.538 Chain F: V.10, A.11, A.14, S.15, A.18, R.19, R.22, S.39, F.40, N.42, C.43, Q.62, F.67, F.71, A.321, N.325, R.329 Ligands: FAD.11 18 PLIP interactions: 8 interactions with chain E, 10 interactions with chain F Hydrogen bonds: E:K.454, E:K.454, E:Q.459, E:N.466, E:V.533, E:N.538, F:F.40, F:N.325 Salt bridges: E:K.454, E:K.454, F:R.19, F:R.22, F:R.22, F:R.329 Hydrophobic interactions: F:V.10, F:A.14, F:Q.62, F:F.67

Links

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Citation

Lee, K.H. et al., Characterization of the mechanism of the NADH-dependent polysulfide reductase (Npsr) from Shewanella loihica PV-4: Formation of a productive NADH-enzyme complex and its role in the general mechanism of NADH and FAD-dependent enzymes. Biochim.Biophys.Acta (2014)

Release Date

2014-08-20

Peptides

FAD-dependent pyridine nucleotide-disulphide oxidoreductase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

FAD-dependent pyridine nucleotide-disulphide oxidoreductase

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