SMTL ID : 2ycp.1

F448H mutant of tyrosine phenol-lyase from Citrobacter freundii in complex with quinonoid intermediate formed with 3-fluoro-L-tyrosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x P61: (2E)-3-(3-fluoro-4-hydroxyphenyl)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}propanoic acid(Non-covalent)

P61.1: 23 residues within 4Å: Chain A: F.36, T.49, S.51, 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, H.448, F.449 Chain B: Y.71 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.123, A:T.125, A:F.449, A:F.449 Hydrogen bonds: A:T.49, 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, A:R.381, A:R.381, A:H.448 Water bridges: A:S.51, A:S.51, A:D.214 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 P61.10: 23 residues within 4Å: Chain A: Y.71 Chain B: F.36, T.49, S.51, 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, H.448, F.449 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.123, B:T.125, B:F.449, B:F.449 Hydrogen bonds: B:T.49, B:Q.98, B:G.99, B:R.100, B:T.124, B:N.185, B:D.214, B:T.216, B:R.217, B:R.217, B:S.254, B:K.257, B:R.381, B:R.381, B:H.448 Water bridges: B:S.51, A:Y.291 Salt bridges: B:R.100, B:R.217, B:K.256, B:K.257, B:K.257, B:R.404 pi-Stacking: B:F.123 P61.17: 23 residues within 4Å: Chain C: F.36, T.49, S.51, 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, H.448, F.449 Chain D: Y.71 26 PLIP interactions: 25 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.123, C:F.449, C:F.449 Hydrogen bonds: C:T.49, 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, C:R.381, C:R.381, C:H.448 Water bridges: C:S.51, C:D.214, D:Y.291 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 P61.26: 23 residues within 4Å: Chain C: Y.71 Chain D: F.36, T.49, S.51, 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, H.448, F.449 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:F.123, D:T.125, D:F.449, D:F.449 Hydrogen bonds: D:T.49, D:S.51, D:Q.98, D:G.99, D:R.100, D:T.124, D:N.185, D:D.214, D:T.216, D:R.217, D:R.217, D:S.254, D:K.257, D:R.381, D:R.381, D:H.448 Water bridges: D:S.51, D:K.256 Salt bridges: D:R.100, D:R.217, D:K.256, D:K.257, D:K.257, D:R.404 pi-Stacking: D:F.123

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

PGE.2: 7 residues within 4Å: Chain A: V.138, D.139, K.162, K.165, L.166, E.169, K.170 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.139 PGE.3: 4 residues within 4Å: Chain A: K.226, E.227, E.233, Y.312 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.226 PGE.4: 6 residues within 4Å: Chain A: Q.311, E.313 Chain D: V.16, S.17, M.18, Y.44 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Water bridges: D:M.18, A:Q.311 PGE.6: 4 residues within 4Å: Chain A: R.388, E.442, K.444 Ligands: PG4.5 No protein-ligand interaction detected (PLIP) PGE.12: 4 residues within 4Å: Chain B: K.226, E.233, Y.312, E.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.226 Water bridges: B:K.226, B:K.226 PGE.15: 7 residues within 4Å: Chain B: K.59, A.62, M.66, I.304 Chain D: K.59, M.66, I.304 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.59 PGE.19: 6 residues within 4Å: Chain B: Q.311, E.313 Chain C: V.16, S.17, M.18, Y.44 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:M.18 Water bridges: C:S.17, C:S.17 PGE.20: 7 residues within 4Å: Chain C: V.138, D.139, K.162, K.165, L.166, E.169, K.170 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.139, C:E.169 PGE.21: 3 residues within 4Å: Chain C: K.226, E.233, Y.312 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.226 Water bridges: C:E.227 PGE.22: 4 residues within 4Å: Chain C: K.444 Chain D: S.277, E.280 Ligands: PEG.23 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.444 Water bridges: C:K.444, C:K.444 PGE.28: 8 residues within 4Å: Chain D: Y.116, V.138, D.139, K.162, K.165, L.166, E.169, K.170 1 PLIP interactions: 1 interactions with chain D Water bridges: D:D.139 PGE.29: 3 residues within 4Å: Chain D: K.226, E.233, Y.312 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.226, D:K.226 Water bridges: D:Y.312 PGE.31: 3 residues within 4Å: Chain D: E.442, K.444 Ligands: PG4.30 No protein-ligand interaction detected (PLIP)

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 4 residues within 4Å: Chain A: K.444 Chain B: S.277, E.280 Ligands: PGE.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.444 PG4.9: 7 residues within 4Å: Chain A: V.16, S.17, M.18, Y.44 Chain D: P.7, Q.311, E.313 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:M.18 Water bridges: A:M.18, D:Q.311 PG4.11: 6 residues within 4Å: Chain B: V.138, D.139, K.162, L.166, E.169, K.170 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.162 PG4.13: 4 residues within 4Å: Chain A: S.277, E.280 Chain B: K.444 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.444 Water bridges: B:K.444 PG4.30: 4 residues within 4Å: Chain C: S.277, E.280 Chain D: K.444 Ligands: PGE.31 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.444

4 x K: POTASSIUM ION(Non-covalent)

K.7: 3 residues within 4Å: Chain A: G.52, N.262 Chain B: E.69 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.69, A:G.52, A:N.262, H2O.4, H2O.31 K.8: 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.13, H2O.23 K.24: 3 residues within 4Å: Chain C: G.52, N.262 Chain D: E.69 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:E.69, C:G.52, C:N.262, H2O.59, H2O.67 K.25: 3 residues within 4Å: Chain C: E.69 Chain D: G.52, N.262 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:G.52, D:N.262, C:E.69, H2O.49, H2O.58

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.14: 3 residues within 4Å: Chain B: E.442, K.444 Ligands: PG4.13 No protein-ligand interaction detected (PLIP)

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.16: 7 residues within 4Å: Chain B: V.16, S.17, M.18, Y.44 Chain C: P.7, Q.311, E.313 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.17 Water bridges: B:M.18, B:Y.44

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

P33.18: 13 residues within 4Å: Chain B: M.1, Y.3, Y.324, Y.414, A.415, D.418, V.419 Chain C: M.1, Y.3, Y.324, Y.414, A.415, D.418 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.324 Water bridges: C:D.418, C:D.418 P33.27: 12 residues within 4Å: Chain A: M.1, Y.3, Y.324, Y.414, A.415, V.419 Chain D: M.1, Y.3, Y.324, Y.414, A.415, D.418 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.324 Water bridges: A:D.418, A:D.418

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.23: 3 residues within 4Å: Chain C: E.442, K.444 Ligands: PGE.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.444 PEG.32: 5 residues within 4Å: Chain D: Q.108, L.109, A.110, I.111, K.112 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Milic, D. et al., Crystallographic Snapshots of Tyrosine Phenol-Lyase Show that Substrate Strain Plays a Role in C-C Bond Cleavage. J.Am.Chem.Soc. (2011)

Release Date

2011-09-14

Peptides

TYROSINE PHENOL-LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

TYROSINE PHENOL-LYASE