SMTL ID : 4m73.1

Mutant structure of methyltransferase from Streptomyces hygroscopicus

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: 16 residues within 4Å: Chain A: S.140, G.166, G.168, R.172, D.189, I.190, A.191, A.194, G.216, D.217, A.218, R.219, F.239, M.240, M.241 Ligands: M72.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.140, A:G.168, A:I.190, A:D.217, A:D.217, A:A.218, A:F.239, A:F.239 Water bridges: A:R.172, A:F.239 Salt bridges: A:R.172 SAH.12: 15 residues within 4Å: Chain B: S.140, G.166, G.168, R.172, D.189, I.190, A.191, A.194, G.216, D.217, A.218, R.219, F.239, M.240, M.241 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.140, B:G.166, B:G.166, B:G.168, B:I.190, B:A.191, B:D.217, B:A.218 Water bridges: B:R.172, B:F.239 Salt bridges: B:R.172

2 x M72: (2R,3R)-2-hydroxy-3-methoxy-3-phenylpropanoic acid(Non-covalent)

M72.2: 12 residues within 4Å: Chain A: W.99, I.132, C.136, M.240, H.243, D.272, A.273, F.287, F.291, H.295 Ligands: SAH.1, FE.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.240, A:A.273, A:F.287, A:F.291 Salt bridges: A:H.243, A:H.295 M72.13: 9 residues within 4Å: Chain B: W.99, I.132, C.136, M.240, H.243, D.272, F.287, H.295 Ligands: FE.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.240, B:F.287 Salt bridges: B:H.243, B:H.295

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

FE.3: 3 residues within 4Å: Chain A: H.243, H.295 Ligands: M72.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.243, A:H.295, H2O.5, H2O.9, H2O.14 FE.14: 4 residues within 4Å: Chain B: H.243, H.295, E.300 Ligands: M72.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.243, B:H.295, B:E.300, H2O.28, H2O.28

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

HF2.4: 7 residues within 4Å: Chain A: D.309, F.312, C.319, V.320, K.321, K.322, F.334 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.309, A:D.309 Water bridges: A:D.309 Salt bridges: A:K.322 HF2.15: 7 residues within 4Å: Chain B: D.309, F.312, C.319, V.320, K.321, K.322, F.334 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.309 Salt bridges: B:K.322

13 x CA: CALCIUM ION(Non-covalent)

CA.5: 1 residues within 4Å: Chain A: R.12 No protein-ligand interaction detected (PLIP) CA.6: 4 residues within 4Å: Chain A: K.44, L.45, D.46, T.80 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: P.85 Chain B: R.282 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain A: P.112, Q.113 Chain B: Q.102 No protein-ligand interaction detected (PLIP) CA.9: 2 residues within 4Å: Chain A: D.306, D.309 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.309, H2O.8, H2O.18 CA.10: 5 residues within 4Å: Chain A: R.109 Chain B: E.106, Q.126, L.127, D.128 No protein-ligand interaction detected (PLIP) CA.16: 1 residues within 4Å: Chain B: R.12 No protein-ligand interaction detected (PLIP) CA.17: 1 residues within 4Å: Chain B: G.78 No protein-ligand interaction detected (PLIP) CA.18: 2 residues within 4Å: Chain A: R.282 Chain B: P.85 No protein-ligand interaction detected (PLIP) CA.19: 3 residues within 4Å: Chain B: K.44, L.45, D.46 No protein-ligand interaction detected (PLIP) CA.20: 2 residues within 4Å: Chain B: P.112, Q.113 No protein-ligand interaction detected (PLIP) CA.21: 3 residues within 4Å: Chain B: K.123, F.124, Y.125 No protein-ligand interaction detected (PLIP) CA.22: 4 residues within 4Å: Chain B: R.215, D.217, Q.223, V.224 No protein-ligand interaction detected (PLIP)

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.11: 3 residues within 4Å: Chain A: D.217, T.220, Q.223 Ligand excluded by 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

2014-06-25

Peptides

Methyltransferase MppJ: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase MppJ