SMTL ID : 5x30.1

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

2 x HCS: 2-AMINO-4-MERCAPTO-BUTYRIC ACID(Non-covalent)

HCS.1: 8 residues within 4Å: Chain A: Y.114, K.211, V.339, S.340, L.341, Q.349, R.375 Chain B: Y.59 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.114 Hydrogen bonds: A:S.340, A:Q.349 Salt bridges: A:R.375 HCS.4: 8 residues within 4Å: Chain C: Y.114, K.211, V.339, S.340, L.341, Q.349, R.375 Chain D: Y.59 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.340, C:Q.349 Water bridges: C:R.375, C:R.375 Salt bridges: C:R.375

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

4LM.2: 19 residues within 4Å: Chain A: Y.59, R.61 Chain B: S.88, G.89, M.90, I.93, Y.114, D.186, T.188, S.208, T.210, K.211, T.220, A.221, V.339, S.340, L.341, R.375 Ligands: H2S.3 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.114, B:V.339, A:Y.59 Hydrogen bonds: B:S.88, B:G.89, B:M.90, B:S.208, B:K.211, B:S.340 Water bridges: B:D.186, B:Y.189, B:R.375 Salt bridges: B:K.211, B:K.211, B:R.375, A:R.61 pi-Stacking: B:Y.114

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.3: 3 residues within 4Å: Chain B: Y.114, H.116 Ligands: 4LM.2 No protein-ligand interaction detected (PLIP)

1 x 7XF: (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-sulfanyl-butanoic acid(Non-covalent)

7XF.5: 19 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, R.375 16 PLIP interactions: 1 interactions with chain C, 15 interactions with chain D Salt bridges: C:R.61, D:K.211, D:K.211, D:R.375 Hydrophobic interactions: D:Y.114, D:T.188 Hydrogen bonds: D:S.88, D:G.89, D:M.90, D:N.161, D:S.208, D:K.211, D:S.340, D:S.340 Water bridges: D:D.186 pi-Stacking: D:Y.114

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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