SMTL ID : 6dyt.1

Citrobacter freundii tyrosine phenol-lyase F448A mutant complexed with L-alanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: G.52, N.262 Chain B: E.69 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.69, A:G.52, H2O.3, H2O.12, H2O.13 K.2: 3 residues within 4Å: Chain A: E.69 Chain B: G.52, N.262 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:E.69, B:G.52, H2O.2, H2O.3, H2O.15 K.6: 3 residues within 4Å: Chain C: G.52, N.262 Chain D: E.69 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:G.52, D:E.69, H2O.27, H2O.36, H2O.37 K.7: 3 residues within 4Å: Chain C: E.69 Chain D: G.52, N.262 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:G.52, C:E.69, H2O.26, H2O.27, H2O.39

2 x F0G: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine(Non-covalent)

F0G.3: 18 residues within 4Å: Chain A: T.49, S.51, Q.98, G.99, R.100, E.103, F.123, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, M.379, R.404 Chain B: Y.71 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.123 Hydrogen bonds: A:T.49, A:S.51, A:Q.98, A:G.99, A:R.100, A:N.185, A:R.217, A:R.217, A:S.254, A:K.257 Water bridges: A:K.256 Salt bridges: A:R.100, A:R.217, A:K.257, A:K.257, A:R.404 pi-Stacking: A:F.123 F0G.8: 18 residues within 4Å: Chain C: T.49, S.51, Q.98, G.99, R.100, E.103, F.123, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, M.379, R.404 Chain D: Y.71 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.123 Hydrogen bonds: C:T.49, C:S.51, C:Q.98, C:G.99, C:R.100, C:N.185, C:R.217, C:R.217, C:S.254, C:K.257 Water bridges: C:K.256, D:Y.71 Salt bridges: C:R.100, C:R.217, C:K.257, C:K.257, C:R.404 pi-Stacking: C:F.123

2 x PP3: ALANYL-PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PP3.4: 16 residues within 4Å: Chain A: Y.71 Chain B: T.49, Q.98, G.99, R.100, E.103, F.123, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, R.404 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.123 Hydrogen bonds: B:T.49, 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, B:K.257 Water bridges: B:E.103, A:Y.71 Salt bridges: B:R.100, B:R.217, B:K.256, B:K.257, B:R.404 pi-Stacking: B:F.123 PP3.9: 16 residues within 4Å: Chain C: Y.71 Chain D: T.49, Q.98, G.99, R.100, E.103, F.123, T.125, N.185, D.214, T.216, R.217, S.254, K.256, K.257, R.404 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.123 Hydrogen bonds: D:T.49, D:S.51, D:Q.98, D:G.99, D:R.100, D:N.185, D:R.217, D:R.217, D:S.254, D:K.257 Salt bridges: D:R.100, D:R.217, D:K.256, D:K.257, D:R.404 pi-Stacking: D:F.123

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

P33.5: 12 residues within 4Å: Chain B: Y.3, Y.324, Y.414, A.415, D.418 Chain C: N.2, Y.3, Y.324, Y.414, A.415, D.418, D.422 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.2 Water bridges: C:Y.3, C:D.422, B:Y.3 P33.10: 12 residues within 4Å: Chain A: N.2, Y.3, Y.324, Y.414, A.415, D.418, D.422 Chain D: Y.3, Y.324, Y.414, A.415, D.418 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:N.2, A:D.422, D:Y.324 Water bridges: A:Y.3, D:D.418, D:D.418, D:D.422, D:D.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism. Biochemistry (2018)

Release Date

2018-10-10

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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