SMTL ID : 3v97.2 (1 other biounit)

Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAH binding

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GLC- TRV: 6-O-octanoyl-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-TRV.1: 10 residues within 4Å: Chain A: M.50, G.218, L.219, H.220, R.221, G.222, W.224, W.237, K.241, Q.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.218, A:W.224, A:K.241, A:H.220, A:Q.245 Water bridges: A:Q.245

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

SAH.2: 17 residues within 4Å: Chain A: I.174, P.197, M.198, C.199, G.200, S.201, G.202, D.263, S.264, D.265, K.290, D.291, V.292, N.310, P.312, L.326 Ligands: GOL.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.201, A:G.202, A:S.264, A:D.291, A:V.292, A:N.310 Water bridges: A:C.199, A:S.201, A:N.310 SAH.3: 15 residues within 4Å: Chain A: F.524, F.547, S.548, Y.549, D.569, M.570, S.571, Y.574, A.597, D.598, C.599, F.614, D.616, P.618, S.621 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.549 Hydrogen bonds: A:Y.549, A:M.570, A:D.598, A:C.599, A:D.616, A:D.616, A:S.621 Water bridges: A:R.531, A:G.551, A:S.552, A:S.552, A:A.553, A:A.553, A:D.616

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: P.173, N.310, P.311, Y.313, N.368 Ligands: SAH.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.310, A:P.311, A:N.368 GOL.5: 3 residues within 4Å: Chain A: F.501, W.577, R.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.580

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, K.T. et al., Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Nucleic Acids Res. (2012)

Release Date

2012-02-29

Peptides

Ribosomal RNA large subunit methyltransferase L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ribosomal RNA large subunit methyltransferase L

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