SMTL ID : 2vlh.1

Quinonoid intermediate of Citrobacter freundii tyrosine phenol-lyase formed with methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

2 x PM9: (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}-4-(METHYLSULFANYL)BUTANOIC ACID(Non-covalent)

PM9.1: 21 residues within 4Å: Chain A: T.49, Q.98, G.99, R.100, E.103, F.123, T.124, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, M.379, R.381, R.404, F.448, F.449 Chain B: Y.71 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.49, A:S.51, A:Q.98, A:G.99, A:R.100, A:N.185, A:D.214, A:R.217, A:R.217, A:S.254, A:K.257 Water bridges: A:S.51, A:T.126, B:Y.71 Salt bridges: A:R.100, A:R.217, A:K.256, A:K.257, A:K.257, A:R.381, A:R.404 pi-Stacking: A:F.123 PM9.7: 21 residues within 4Å: Chain C: T.49, Q.98, G.99, R.100, E.103, F.123, T.124, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, M.379, R.381, R.404, F.448, F.449 Chain D: Y.71 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.49, C:S.51, C:Q.98, C:G.99, C:R.100, C:N.185, C:D.214, C:R.217, C:R.217, C:S.254, C:K.257 Water bridges: C:S.51, C:T.126, D:Y.71 Salt bridges: C:R.100, C:R.217, C:K.256, C:K.257, C:K.257, C:R.381, C:R.404 pi-Stacking: C:F.123

4 x K: POTASSIUM ION(Non-covalent)

K.2: 3 residues within 4Å: Chain A: G.52, N.262 Chain B: E.69 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:G.52, A:N.262, B:E.69, H2O.4, H2O.29 K.6: 3 residues within 4Å: Chain A: E.69 Chain B: G.52, N.262 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.52, B:N.262, A:E.69, H2O.4, H2O.12 K.8: 3 residues within 4Å: Chain C: G.52, N.262 Chain D: E.69 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:G.52, C:N.262, D:E.69, H2O.38, H2O.63 K.12: 3 residues within 4Å: Chain C: E.69 Chain D: G.52, N.262 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.69, D:G.52, D:N.262, H2O.38, H2O.46

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

PGE.3: 3 residues within 4Å: Chain A: K.226, E.233, Y.312 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.226 Water bridges: A:E.227, A:Y.312 PGE.9: 3 residues within 4Å: Chain C: K.226, E.233, Y.312 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.226 Water bridges: C:E.227, C:Y.312

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.4: 14 residues within 4Å: Chain A: M.1, Y.3, A.5, Y.324, Y.414, A.415, D.418 Chain D: Y.3, Y.324, Y.414, A.415, D.418, V.419, D.422 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.324 P33.10: 14 residues within 4Å: Chain B: Y.3, Y.324, Y.414, A.415, D.418, V.419, D.422 Chain C: M.1, Y.3, A.5, Y.324, Y.414, A.415, D.418 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.324

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.5: 14 residues within 4Å: Chain B: Q.98, G.99, R.100, E.103, F.123, T.125, T.126, N.185, D.214, T.216, R.217, S.254, K.256, K.257 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.123, B:F.123, B:K.257 Hydrogen bonds: B:S.51, B:S.51, B:Q.98, B:G.99, B:R.100, B:N.185, B:T.216, B:R.217, B:R.217, B:S.254 Water bridges: B:R.100, B:E.103, B:K.256 Salt bridges: B:R.100, B:K.256, B:K.257 pi-Stacking: B:F.123 PLP.11: 14 residues within 4Å: Chain D: Q.98, G.99, R.100, E.103, F.123, T.125, T.126, N.185, D.214, T.216, R.217, S.254, K.256, K.257 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:F.123, D:F.123, D:K.257 Hydrogen bonds: D:S.51, D:S.51, D:Q.98, D:G.99, D:R.100, D:N.185, D:T.216, D:R.217, D:R.217, D:S.254 Water bridges: D:R.100, D:E.103, D:K.256, D:K.257 Salt bridges: D:R.100, D:K.256, D:K.257 pi-Stacking: D:F.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milic, D. et al., Insights Into the Catalytic Mechanism of Tyrosine Phenol-Lyase from X-Ray Structures of Quinonoid Intermediates. J.Biol.Chem. (2008)

Release Date

2008-08-19

Peptides

TYROSINE PHENOL-LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

TYROSINE PHENOL-LYASE

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