SMTL ID : 6nv8.1

Perdeuterated tyrosine phenol-lyase from Citrobacter freundii complexed with an aminoacrylate intermediate formed from S-ethyl-L-cysteine and 4-hydroxypyridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 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 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:G.52, B:E.69, H2O.3, H2O.7 K.5: 3 residues within 4Å: Chain A: E.69 Chain B: G.52, N.262 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.52, A:E.69, H2O.2, H2O.8 K.9: 3 residues within 4Å: Chain C: G.52, N.262 Chain D: E.69 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.69, C:G.52, H2O.13, H2O.17 K.13: 3 residues within 4Å: Chain C: E.69 Chain D: G.52, N.262 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.69, D:G.52, H2O.12, H2O.18

6 x CQG: pyridin-4-ol(Non-covalent)

CQG.2: 3 residues within 4Å: Chain A: E.227, Q.228, R.323 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.228 CQG.3: 9 residues within 4Å: Chain A: R.100, F.123, T.124, T.125, R.381, F.448, F.449 Chain B: Y.71 Ligands: 0JO.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.123, A:T.125, A:F.448 Hydrogen bonds: A:R.100, A:R.381, A:R.381, B:Y.71 pi-Stacking: A:F.449 CQG.6: 9 residues within 4Å: Chain A: D.68 Chain B: E.14, T.15, V.16, S.17, S.40, K.41, I.43 Chain C: R.9 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.41 Hydrogen bonds: B:S.17, B:K.41 CQG.10: 3 residues within 4Å: Chain C: E.227, Q.228, R.323 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Q.228 Hydrogen bonds: C:E.227 CQG.11: 9 residues within 4Å: Chain C: R.100, F.123, T.124, T.125, R.381, F.448, F.449 Chain D: Y.71 Ligands: 0JO.12 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.123, C:T.125, C:F.448 Hydrogen bonds: C:R.100, C:T.124, C:T.124, C:R.381, C:R.381 pi-Stacking: C:F.449 CQG.14: 9 residues within 4Å: Chain A: R.9 Chain C: D.68 Chain D: E.14, T.15, V.16, S.17, S.40, K.41, I.43 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.41 Hydrogen bonds: D:E.14, D:S.17, D:S.17

2 x 0JO: 2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid(Non-covalent)

0JO.4: 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, R.404 Chain B: Y.71 Ligands: CQG.3 19 PLIP interactions: 19 interactions with chain A 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:S.254, A:K.257 Water bridges: A:K.256 Salt bridges: A:R.100, A:R.217, A:K.256, A:K.257, A:K.257, A:R.404 pi-Stacking: A:F.123 0JO.12: 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, R.404 Chain D: Y.71 Ligands: CQG.11 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:S.51, C:Q.98, C:G.99, C:R.100, C:N.185, C:T.216, C:R.217, C:R.217, C:S.254, C:S.254, C:K.257 Water bridges: C:K.256 Salt bridges: C:R.100, C:R.217, C:K.256, C:K.257, C:K.257, C:R.404 pi-Stacking: C:F.123

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

P33.7: 13 residues within 4Å: Chain B: N.2, Y.3, Y.324, A.415, D.418, V.419 Chain C: Y.3, A.5, Y.324, Y.414, A.415, D.418, D.422 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:D.418, C:Y.324 P33.15: 13 residues within 4Å: Chain A: Y.3, A.5, Y.324, Y.414, A.415, D.418, D.422 Chain D: N.2, Y.3, Y.324, A.415, D.418, V.419 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.418

2 x DHA: 2-AMINO-ACRYLIC ACID(Covalent)

DHA.8: 9 residues within 4Å: Chain A: Y.71 Chain B: T.49, S.51, R.100, F.123, N.185, R.217, K.257, R.404 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.49, B:N.185 Salt bridges: B:R.217, B:R.404 DHA.16: 9 residues within 4Å: Chain C: Y.71 Chain D: T.49, S.51, R.100, F.123, N.185, R.217, K.257, R.404 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.49, D:N.185 Salt bridges: D:R.217, D:R.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phillips, R.S. et al., Pressure and Temperature Effects on the Formation of Aminoacrylate Intermediates of Tyrosine Phenol-lyase Demonstrate Reaction Dynamics. Acs Catalysis (2020)

Release Date

2020-02-12

Peptides

Tyrosine phenol-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tyrosine phenol-lyase

Related Entries With Identical Sequence