SMTL ID : 5k30.1

Crystal structure of methionine gamma-lyase from Citrobacter freundii modified by S-Ethyl-L-cysteine sulfoxide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-tetramer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, I.219, G.220, L.340 Chain C: R.60 14 PLIP interactions: 1 interactions with chain C, 13 interactions with chain A Salt bridges: C:R.60, A:K.210 Hydrophobic interactions: A:Y.113, A:F.188, A:K.210 Hydrogen bonds: A:G.88, A:I.89, A:Y.113, A:T.187, A:S.207, A:T.209, A:K.210, A:G.220 pi-Stacking: A:Y.113 PLP.7: 15 residues within 4Å: Chain B: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, I.219, G.220, L.340 Chain D: R.60 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:Y.113, B:F.188, B:K.210 Hydrogen bonds: B:G.88, B:I.89, B:Y.113, B:T.187, B:S.207, B:T.209, B:K.210, B:G.220 Salt bridges: B:K.210, D:R.60 pi-Stacking: B:Y.113 PLP.13: 15 residues within 4Å: Chain A: R.60 Chain C: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, I.219, G.220, L.340 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.113, C:F.188, C:K.210 Hydrogen bonds: C:G.88, C:I.89, C:Y.113, C:S.207, C:G.220 Water bridges: C:E.156 Salt bridges: C:K.210, A:R.60 pi-Stacking: C:Y.113 PLP.19: 15 residues within 4Å: Chain B: R.60 Chain D: S.87, G.88, I.89, Y.113, E.156, D.185, T.187, F.188, S.207, T.209, K.210, I.219, G.220, L.340 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain D Salt bridges: B:R.60, D:K.210 Hydrophobic interactions: D:Y.113, D:F.188, D:K.210 Hydrogen bonds: D:G.88, D:I.89, D:Y.113, D:S.207, D:G.220 Water bridges: D:E.156 pi-Stacking: D:Y.113

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

1PE.2: 11 residues within 4Å: Chain A: P.191, Y.192, C.193, Q.195, E.266, Q.303, R.304, Q.305, M.306, S.307, L.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.307 Water bridges: A:Q.195, A:Q.303, A:M.306 1PE.8: 11 residues within 4Å: Chain B: P.191, Y.192, C.193, Q.195, E.266, Q.303, R.304, Q.305, M.306, S.307, L.308 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.307 Water bridges: B:Q.195, B:Q.303, B:M.306 1PE.14: 11 residues within 4Å: Chain C: P.191, Y.192, C.193, Q.195, E.266, Q.303, R.304, Q.305, M.306, S.307, L.308 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.307 Water bridges: C:Q.195, C:Q.303, C:M.306 1PE.20: 11 residues within 4Å: Chain D: P.191, Y.192, C.193, Q.195, E.266, Q.303, R.304, Q.305, M.306, S.307, L.308 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.307 Water bridges: D:Q.195, D:Q.303, D:M.306

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

PEG.3: 2 residues within 4Å: Chain A: E.322, R.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.326, A:R.326 PEG.9: 2 residues within 4Å: Chain B: E.322, R.326 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.326, B:R.326 PEG.15: 2 residues within 4Å: Chain C: E.322, R.326 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.326, C:R.326 PEG.21: 2 residues within 4Å: Chain D: E.322, R.326 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.326, D:R.326

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

PGE.4: 3 residues within 4Å: Chain A: F.278, N.387, E.390 No protein-ligand interaction detected (PLIP) PGE.5: 4 residues within 4Å: Chain A: E.270, K.274, P.382, E.383 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.274, A:E.383 PGE.10: 3 residues within 4Å: Chain B: F.278, N.387, E.390 No protein-ligand interaction detected (PLIP) PGE.11: 4 residues within 4Å: Chain B: E.270, K.274, P.382, E.383 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.274, B:E.383 PGE.16: 3 residues within 4Å: Chain C: F.278, N.387, E.390 No protein-ligand interaction detected (PLIP) PGE.17: 4 residues within 4Å: Chain C: E.270, K.274, P.382, E.383 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.274, C:E.383 Water bridges: C:E.270 PGE.22: 3 residues within 4Å: Chain D: F.278, N.387, E.390 No protein-ligand interaction detected (PLIP) PGE.23: 4 residues within 4Å: Chain D: E.270, K.274, P.382, E.383 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.274, D:E.383 Water bridges: D:E.270

4 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 3 residues within 4Å: Chain A: E.390, H.391, R.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.391, A:R.394 Water bridges: A:R.394 TRS.12: 3 residues within 4Å: Chain B: E.390, H.391, R.394 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.391, B:R.394 Water bridges: B:R.394 TRS.18: 3 residues within 4Å: Chain C: E.390, H.391, R.394 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.391, C:R.394 Water bridges: C:R.394 TRS.24: 3 residues within 4Å: Chain D: E.390, H.391, R.394 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.391, D:R.394 Water bridges: D:R.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Revtovich, S. et al., Sulfoxides of sulfur-containing amino acids are suicide substrates of Citrobacter freundii methionine gamma-lyase. Structural bases of the enzyme inactivation. Biochimie (2020)

Release Date

2017-07-12

Peptides

Methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Methionine gamma-lyase

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