SMTL ID : 3ayl.1

X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from Pseudomonas sp. P501. Structures of the enzyme-ligand complex and catalytic mechanism

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: R.475, T.543, R.546, T.609 Chain B: R.475, T.543, R.546, T.609 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.475, A:R.546, B:R.475, B:R.546 SO4.2: 2 residues within 4Å: Chain A: R.599, T.600 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.600, A:T.600, A:T.600 Water bridges: A:A.601

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

FAD.3: 40 residues within 4Å: Chain A: V.62, G.63, G.64, G.65, A.66, G.67, Y.93, E.94, A.95, D.96, G.118, R.119, V.120, V.139, G.140, A.141, M.142, R.143, F.144, E.372, R.373, V.374, A.409, V.410, P.411, Q.414, I.418, S.476, Y.536, W.608, G.616, F.617, S.651, D.652, G.659, W.660, L.661, A.664 Ligands: MET.4, GOL.5 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:R.119, A:W.608 Hydrogen bonds: A:G.64, A:A.66, A:G.67, A:A.95, A:D.96, A:G.118, A:R.119, A:A.141, A:M.142, A:R.143, A:R.143, A:V.374, A:V.374, A:D.652, A:D.652, A:D.652, A:L.661 Water bridges: A:G.64, A:G.65, A:G.68, A:E.94, A:E.94, A:E.94, A:V.120, A:V.120, A:R.373, A:Q.414, A:Q.414, A:Q.414, A:Q.414, A:Y.536, A:E.662 Salt bridges: A:R.119, A:R.119 pi-Stacking: A:F.617, A:W.660 FAD.6: 40 residues within 4Å: Chain B: V.62, G.63, G.64, G.65, A.66, G.67, Y.93, E.94, A.95, D.96, G.118, R.119, V.120, V.139, G.140, A.141, M.142, R.143, F.144, E.372, R.373, V.374, A.409, V.410, P.411, Q.414, I.418, S.476, Y.536, W.608, G.616, F.617, S.651, D.652, G.659, W.660, L.661, A.664 Ligands: MET.7, GOL.8 36 PLIP interactions: 36 interactions with chain B Hydrophobic interactions: B:R.119, B:W.608 Hydrogen bonds: B:G.64, B:A.66, B:G.67, B:A.95, B:D.96, B:G.118, B:R.119, B:A.141, B:M.142, B:R.143, B:R.143, B:V.374, B:V.374, B:D.652, B:D.652, B:L.661 Water bridges: B:G.64, B:G.65, B:G.68, B:E.94, B:E.94, B:D.96, B:V.120, B:V.120, B:R.373, B:Q.414, B:Q.414, B:Q.414, B:Q.414, B:E.662 Salt bridges: B:R.119, B:R.119 pi-Stacking: B:F.617, B:W.660

2 x MET: METHIONINE(Non-covalent)

MET.4: 9 residues within 4Å: Chain A: R.143, Y.536, W.538, F.617, L.619, G.658, G.659, W.660 Ligands: FAD.3 8 PLIP interactions: 2 Ligand-Ligand interactions, 6 interactions with chain A Hydrogen bonds: M.4, M.4, A:Y.536, A:G.659 Hydrophobic interactions: A:F.617 Water bridges: A:R.143, A:R.143 Salt bridges: A:R.143 MET.7: 9 residues within 4Å: Chain B: R.143, Y.536, W.538, F.617, L.619, G.658, G.659, W.660 Ligands: FAD.6 7 PLIP interactions: 5 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:F.617 Hydrogen bonds: B:G.659, M.7, M.7 Water bridges: B:R.143, B:R.143 Salt bridges: B:R.143

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: A.95, D.96, Q.414, N.611, K.612 Ligands: FAD.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.414, A:N.611 Water bridges: A:N.611, A:N.611, A:K.612 GOL.8: 6 residues within 4Å: Chain B: A.95, D.96, Q.414, N.611, K.612 Ligands: FAD.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.414, B:N.611 Water bridges: B:N.611, B:N.611, B:K.612, B:K.612

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ida, K. et al., High resolution X-ray crystal structures of L-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. P-501. Structures of the enzyme-ligand complex and catalytic mechanism. J.Biochem. (2011)

Release Date

2011-08-31

Peptides

Pro-enzyme of L-phenylalanine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pro-enzyme of L-phenylalanine oxidase

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