SMTL ID : 2yct.1

Tyrosine phenol-lyase from Citrobacter freundii in complex with pyridine N-oxide and the quinonoid intermediate formed with L-alanine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)(Covalent)

PLP.1: 17 residues within 4Å: Chain A: 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 Ligands: PLI.2, 9PO.4, PO4.6 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.98, A:G.99, A:R.100, A:N.185, A:R.217, A:R.217, A:S.254, A:S.254 Water bridges: A:S.51, A:D.214, B:Y.291, B:Y.291 Salt bridges: A:R.100, A:K.256, A:K.257 pi-Stacking: A:F.123 PLP.7: 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 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.123, B:K.257 Hydrogen bonds: 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:S.51, B:S.51, B:S.51 Salt bridges: B:R.100, B:K.256, B:K.257 pi-Stacking: B:F.123 PLP.11: 17 residues within 4Å: Chain C: 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 Ligands: PLI.12, 9PO.14, PO4.16 16 PLIP interactions: 14 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.98, C:G.99, C:R.100, C:N.185, C:R.217, C:R.217, C:S.254, C:S.254 Water bridges: C:S.51, C:D.214, D:Y.291, D:Y.291 Salt bridges: C:R.100, C:K.256, C:K.257 pi-Stacking: C:F.123 PLP.17: 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 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.123, D:K.257 Hydrogen bonds: 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:S.51, D:S.51, D:S.51 Salt bridges: D:R.100, D:K.256, D:K.257 pi-Stacking: D:F.123

2 x PLI: (2E)-2-{[(Z)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4(1H)-YLIDENE}METHYL]IMINO}PROPANOIC ACID(Covalent)

PLI.2: 20 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 Ligands: PLP.1, 9PO.4, PO4.6 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.123 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 Water bridges: A:S.51, A:S.51, A:R.100, B:Y.291 Salt bridges: A:R.100, A:R.217, A:K.256, A:K.257, A:K.257, A:R.381, A:R.404 PLI.12: 20 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 Ligands: PLP.11, 9PO.14, PO4.16 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.123 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 Water bridges: C:S.51, C:S.51, C:R.100, D:Y.291 Salt bridges: C:R.100, C:R.217, C:K.256, C:K.257, C:K.257, C:R.381, C:R.404

4 x K: POTASSIUM ION(Non-covalent)

K.3: 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.3, H2O.26 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.4, H2O.10 K.13: 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.34, H2O.56 K.18: 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.34, H2O.41

6 x 9PO: PYRIDINE-N-OXIDE(Non-covalent)

9PO.4: 11 residues within 4Å: Chain A: R.100, F.123, T.124, M.379, R.381, F.448, F.449 Chain B: Y.71 Ligands: PLP.1, PLI.2, PO4.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.381, A:R.381 pi-Stacking: A:F.449 Hydrophobic interactions: B:Y.71 9PO.5: 7 residues within 4Å: Chain A: S.12, W.61 Chain B: M.65 Chain C: M.65 Chain D: K.11, S.12, W.61 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:W.61, A:W.61, D:W.61 Hydrogen bonds: A:S.12 pi-Stacking: D:W.61 9PO.10: 6 residues within 4Å: Chain B: A.148, G.149, I.336, V.337, D.348, L.400 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.337, B:D.348 9PO.14: 11 residues within 4Å: Chain C: R.100, F.123, T.124, M.379, R.381, F.448, F.449 Chain D: Y.71 Ligands: PLP.11, PLI.12, PO4.16 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:Y.71 Hydrogen bonds: C:R.381, C:R.381 pi-Stacking: C:F.449 9PO.15: 7 residues within 4Å: Chain A: M.65 Chain B: K.11, S.12, W.61 Chain C: S.12, W.61 Chain D: M.65 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.61, C:W.61, C:W.61 pi-Stacking: B:W.61 Hydrogen bonds: C:S.12 9PO.20: 6 residues within 4Å: Chain D: A.148, G.149, I.336, V.337, D.348, L.400 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.337, D:D.348

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 11 residues within 4Å: Chain A: T.49, F.123, N.185, R.217, K.257, M.379, R.381, R.404 Ligands: PLP.1, PLI.2, 9PO.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.49, A:N.185, A:R.381 Water bridges: A:K.257 Salt bridges: A:R.217, A:K.257, A:R.404 PO4.16: 11 residues within 4Å: Chain C: T.49, F.123, N.185, R.217, K.257, M.379, R.381, R.404 Ligands: PLP.11, PLI.12, 9PO.14 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.49, C:N.185, C:R.381 Water bridges: C:K.257 Salt bridges: C:R.217, C:K.257, C:R.404

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

P33.9: 11 residues within 4Å: Chain B: Y.3, Y.324, Y.414, A.415, D.418 Chain C: Y.3, Y.324, Y.414, A.415, D.418, V.419 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:A.415 Water bridges: B:N.2, B:N.2, B:A.5, B:Y.324, C:D.418, C:D.418 P33.19: 11 residues within 4Å: Chain A: Y.3, Y.324, Y.414, A.415, D.418, V.419 Chain D: Y.3, Y.324, Y.414, A.415, D.418 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.415 Water bridges: D:N.2, D:N.2, D:A.5, D:Y.324, A:D.418, A:D.418

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

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