SMTL ID : 2ycn.1

Y71F 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 2.04 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.17, H2O.24 K.5: 3 residues within 4Å: Chain A: E.69 Chain B: G.52, N.262 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.69, B:G.52, B:N.262, H2O.9 K.7: 3 residues within 4Å: Chain C: G.52, N.262 Chain D: E.69 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:G.52, D:E.69, H2O.46, H2O.53 K.11: 3 residues within 4Å: Chain C: E.69 Chain D: G.52, N.262 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:E.69, D:G.52, D:N.262, H2O.38

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)

P61.2: 22 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, F.448 Chain B: F.71 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.123, A:T.125, B:F.71, B:F.71 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, A:R.381, A:R.381 Water bridges: A:D.214, A:K.256, B:Y.291 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 P61.6: 19 residues within 4Å: Chain A: F.71 Chain B: 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.381, R.404 23 PLIP interactions: 2 interactions with chain A, 21 interactions with chain B Hydrophobic interactions: A:F.71 Water bridges: A:Y.291, B:E.103, B:K.256, B:R.381 Hydrogen bonds: B:S.51, B:Q.98, B:G.99, B:R.100, B:N.185, B:D.214, B:T.216, B:R.217, B:R.217, B:S.254, B:K.257 Salt bridges: B:R.100, B:R.217, B:K.256, B:K.257, B:R.404 pi-Stacking: B:F.123, B:F.123 P61.8: 22 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, F.448 Chain D: F.71 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:F.123, C:T.125, D:F.71, D:F.71 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, C:R.381, C:R.381 Water bridges: C:D.214, C:K.256, 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 P61.12: 19 residues within 4Å: Chain C: F.71 Chain D: 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.381, R.404 23 PLIP interactions: 2 interactions with chain C, 21 interactions with chain D Hydrophobic interactions: C:F.71 Water bridges: C:Y.291, D:E.103, D:K.256, D:R.381 Hydrogen bonds: D:S.51, D:Q.98, D:G.99, D:R.100, D:N.185, D:D.214, D:T.216, 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, D:F.123

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

PG4.3: 11 residues within 4Å: Chain A: M.1, Y.3, A.5, Y.324, Y.414, D.418 Chain D: A.415, D.418, V.419, D.422 Ligands: PEG.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:Y.324 Water bridges: A:A.5, D:V.419 PG4.9: 11 residues within 4Å: Chain B: A.415, D.418, V.419, D.422 Chain C: M.1, Y.3, A.5, Y.324, Y.414, D.418 Ligands: PEG.10 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.324 Water bridges: C:A.5, B:V.419

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

PEG.4: 8 residues within 4Å: Chain A: A.415, D.418 Chain D: M.1, Y.3, A.5, Y.324, Y.414 Ligands: PG4.3 No protein-ligand interaction detected (PLIP) PEG.10: 8 residues within 4Å: Chain B: M.1, Y.3, A.5, Y.324, Y.414 Chain C: A.415, D.418 Ligands: PG4.9 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
A

D
B

TYROSINE PHENOL-LYASE