SMTL ID : 3pfg.1

X-Ray crystal structure the N,N-dimethyltransferase TylM1 from Streptomyces fradiae in complex with SAM and dTDP-phenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

2 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 19 residues within 4Å: Chain A: Y.14, Y.22, Y.33, A.58, C.59, G.60, H.64, E.79, L.80, S.81, M.84, G.100, D.101, M.102, M.117, F.118, S.120, H.123 Ligands: TLO.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.22, A:Y.22, A:Y.33, A:A.58, A:L.80, A:S.81, A:D.101, A:D.101, A:M.102, A:S.120 Water bridges: A:G.62, A:H.64, A:H.64, A:M.117 Salt bridges: A:K.31, A:H.64 SAM.4: 19 residues within 4Å: Chain B: Y.14, Y.22, Y.33, A.58, C.59, G.60, H.64, E.79, L.80, S.81, M.84, G.100, D.101, M.102, M.117, F.118, S.120, H.123 Ligands: TLO.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.22, B:A.58, B:L.80, B:S.81, B:D.101, B:M.102, B:S.120 Water bridges: B:G.62, B:M.117 Salt bridges: B:K.31, B:H.64

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: Y.14, Y.22, H.26, R.177, V.192, E.208, H.210 Ligands: TLO.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.26, A:R.177, A:R.177, A:E.208 EDO.5: 8 residues within 4Å: Chain B: Y.14, Y.22, H.26, R.177, V.192, E.208, H.210 Ligands: TLO.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.26, B:R.177, B:R.177, B:E.208 Water bridges: B:Y.194, B:Y.194

2 x TLO: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine(Non-covalent)

TLO.3: 17 residues within 4Å: Chain A: H.26, K.29, F.118, W.152, W.153, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, I.190, I.212, R.241 Ligands: SAM.1, EDO.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:W.152, A:W.153, A:F.158, A:Y.162, A:I.190, A:I.212 Hydrogen bonds: A:T.159, A:T.159, A:R.177, A:S.179 Water bridges: A:K.29, A:T.159, A:Y.162, A:Y.162, A:R.241, A:R.241, A:R.241 Salt bridges: A:H.26, A:K.29, A:K.29, A:R.177, A:R.241 pi-Stacking: A:F.118, A:W.153, A:Y.162 TLO.6: 17 residues within 4Å: Chain B: H.26, K.29, F.118, W.152, W.153, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, I.190, I.212, R.241 Ligands: SAM.4, EDO.5 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:W.152, B:W.153, B:F.158, B:Y.162, B:I.190, B:I.212 Hydrogen bonds: B:T.159, B:R.177, B:S.179 Water bridges: B:K.29, B:T.159, B:R.241, B:R.241, B:R.241 Salt bridges: B:H.26, B:K.29, B:K.29, B:R.177, B:R.241 pi-Stacking: B:F.118, B:W.153, B:Y.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carney, A.E. et al., Molecular Architecture of TylM1 from Streptomyces fradiae: An N,N-Dimethyltransferase Involved in the Production of dTDP-d-mycaminose . Biochemistry (2011)

Release Date

2010-12-15

Peptides

N-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-methyltransferase

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