SMTL ID : 4kib.1

Crystal structure of methyltransferase from Streptomyces hygroscopicus complexed with S-adenosyl-L-homocysteine and methylphenylpyruvic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 18 residues within 4Å: Chain A: C.156, G.186, S.187, G.188, R.192, D.209, I.210, A.211, A.214, G.236, D.237, A.238, R.239, F.259, M.260, M.261, D.264 Ligands: 56D.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:S.153, A:G.186, A:G.188, A:I.210, A:D.237, A:D.237, A:A.238, A:F.259 Water bridges: A:S.160, A:S.160, A:R.192, A:F.259 Salt bridges: A:R.192 SAH.8: 19 residues within 4Å: Chain B: C.156, S.160, G.186, S.187, G.188, R.192, D.209, I.210, A.211, A.214, G.236, D.237, A.238, R.239, F.259, M.260, M.261, D.264 Ligands: 56D.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.153, B:G.186, B:G.188, B:I.210, B:D.237, B:A.238 Water bridges: B:G.190, B:F.259 Salt bridges: B:R.192

2 x 56D: (3R)-2-oxo-3-phenylbutanoic acid(Non-covalent)

56D.2: 12 residues within 4Å: Chain A: W.119, R.147, C.156, M.260, H.263, D.292, A.293, F.307, F.311, H.315 Ligands: SAH.1, FE.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.293, A:F.307, A:F.311 Water bridges: A:R.147 Salt bridges: A:R.147, A:H.315 56D.9: 13 residues within 4Å: Chain B: W.119, R.147, C.156, M.260, H.263, D.292, A.293, F.307, F.311, H.315, L.348 Ligands: SAH.8, FE.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.293, B:F.307, B:F.311, B:L.348 Hydrogen bonds: B:W.119 Water bridges: B:R.147, B:R.147 Salt bridges: B:R.147, B:H.315

2 x FE: FE (III) ION(Non-covalent)

FE.3: 4 residues within 4Å: Chain A: H.263, D.264, H.315 Ligands: 56D.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.263, A:H.315, H2O.6, H2O.6 FE.10: 3 residues within 4Å: Chain B: H.263, H.315 Ligands: 56D.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.263, B:H.315, H2O.18, H2O.18

2 x HF2: (2R)-2-hydroxy-3-phenylpropanoic acid(Covalent)

HF2.4: 7 residues within 4Å: Chain A: D.329, F.332, C.339, V.340, K.341, K.342, F.354 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.342 Hydrogen bonds: A:D.329, A:D.329 Salt bridges: A:K.342 HF2.11: 7 residues within 4Å: Chain B: D.329, F.332, C.339, V.340, K.341, K.342, F.354 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.329 Salt bridges: B:K.342

5 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: G.236, D.237 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain A: T.178, F.200, P.201, G.202 No protein-ligand interaction detected (PLIP) CA.7: 5 residues within 4Å: Chain A: E.126, Q.146, R.147, D.148 Chain B: R.129 No protein-ligand interaction detected (PLIP) CA.12: 2 residues within 4Å: Chain B: D.326, D.329 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.326, B:D.329, H2O.17 CA.13: 3 residues within 4Å: Chain B: K.64, L.65, D.66 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zou, X.W. et al., Structure and mechanism of a nonhaem-iron SAM-dependent C-methyltransferase and its engineering to a hydratase and an O-methyltransferase. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-05-07

Peptides

Methyltransferase MppJ: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase MppJ

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