SMTL ID : 5x2x.1

Crystal structure of Pseudomonas putida methionine gamma-lyase wild type with L-homocysteine intermediates

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x 4LM: (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid(Non-covalent)

4LM.1: 20 residues within 4Å: Chain A: S.88, G.89, M.90, I.93, Y.114, N.161, D.186, T.188, S.208, T.210, K.211, A.221, V.339, S.340, L.341, T.355, R.375 Chain B: Y.59, R.61 Ligands: H2S.2 17 PLIP interactions: 2 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:Y.59, A:Y.114, A:Y.114, A:V.339 Salt bridges: B:R.61, A:K.211, A:K.211, A:R.375 Hydrogen bonds: A:S.88, A:G.89, A:M.90, A:N.161, A:S.208, A:K.211, A:S.340, A:T.355 Water bridges: A:T.117 4LM.3: 21 residues within 4Å: Chain A: Y.59, R.61 Chain B: S.88, G.89, M.90, I.93, Y.114, N.161, D.186, T.188, S.208, T.210, K.211, T.220, A.221, V.339, S.340, L.341, T.355, R.375 Ligands: H2S.4 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.114, B:Y.114, B:V.339, A:Y.59 Hydrogen bonds: B:G.89, B:M.90, B:N.161, B:N.161, B:T.188, B:S.208, B:T.210, B:K.211, B:S.340, A:Y.59 Salt bridges: B:K.211, B:K.211, B:R.375, A:R.61 4LM.5: 20 residues within 4Å: Chain C: S.88, G.89, M.90, I.93, Y.114, N.161, D.186, T.188, S.208, T.210, K.211, A.221, V.339, S.340, L.341, T.355, R.375 Chain D: Y.59, R.61 Ligands: H2S.6 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:Y.114, C:Y.114, C:V.339, D:Y.59, D:Y.59 Hydrogen bonds: C:S.88, C:G.89, C:M.90, C:N.161, C:S.208, C:K.211, C:S.340 Water bridges: C:E.157 Salt bridges: C:K.211, C:K.211, C:R.375, D:R.61 4LM.7: 21 residues within 4Å: Chain C: Y.59, R.61 Chain D: S.88, G.89, M.90, I.93, Y.114, N.161, D.186, T.188, S.208, T.210, K.211, T.220, A.221, V.339, S.340, L.341, T.355, R.375 Ligands: H2S.8 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.114, D:V.339, C:Y.59, C:Y.59 Hydrogen bonds: D:G.89, D:M.90, D:N.161, D:N.161, D:T.188, D:S.208, D:T.210, D:K.211, D:S.340, C:Y.59 Salt bridges: D:K.211, D:K.211, D:R.375, C:R.61 pi-Stacking: D:Y.114

4 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.2: 3 residues within 4Å: Chain A: Y.114 Chain B: F.50 Ligands: 4LM.1 No protein-ligand interaction detected (PLIP) H2S.4: 3 residues within 4Å: Chain A: F.50 Chain B: Y.114 Ligands: 4LM.3 No protein-ligand interaction detected (PLIP) H2S.6: 3 residues within 4Å: Chain C: Y.114 Chain D: F.50 Ligands: 4LM.5 No protein-ligand interaction detected (PLIP) H2S.8: 3 residues within 4Å: Chain D: Y.114, T.355 Ligands: 4LM.7 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, D. et al., Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis. Protein Sci. (2017)

Release Date

2017-04-12

Peptides

L-methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-methionine gamma-lyase

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