SMTL ID : 6j24.1

Crystal structure of a SAM-dependent methyltransferase LepI in complex with its substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

2 x BYO: (3~{S},4'~{R},4'~{a}~{S},6'~{R},8'~{a}~{S})-4',6'-dimethyl-5-phenyl-spiro[1~{H}-pyridine-3,5'-2,3,4,4~{a},6,8~{a}-hexahydro-1~{H}-naphthalene]-2,4-dione(Non-covalent)

BYO.1: 8 residues within 4Å: Chain A: H.133, L.138, C.175, R.295, D.296, T.338, C.341, A.345 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.138, A:T.338, A:A.345 Hydrogen bonds: A:R.295, A:D.296 pi-Stacking: A:H.133 BYO.3: 12 residues within 4Å: Chain A: M.45, S.48, L.49 Chain B: G.130, H.133, L.138, C.175, F.189, D.296, C.341, I.342, A.345 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.138, B:F.189, B:I.342, B:A.345, A:L.49 pi-Stacking: B:H.133

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

SAM.2: 14 residues within 4Å: Chain A: L.193, G.227, G.228, G.229, D.252, L.253, V.256, H.274, N.275, F.276, H.277, R.291, L.292, I.293 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.227, A:N.275, A:F.276, A:R.291 Water bridges: A:R.291 Salt bridges: A:R.291 pi-Stacking: A:F.276 SAM.4: 14 residues within 4Å: Chain B: L.193, G.227, G.228, G.229, D.252, L.253, V.256, H.274, N.275, F.276, H.277, R.291, L.292, I.293 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.227, B:L.253, B:N.275, B:F.276, B:R.291 Water bridges: B:N.275, B:R.291, B:R.291, B:R.291 Salt bridges: B:R.291 pi-Stacking: B:F.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sun, Q. et al., Deciphering the regulatory and catalytic mechanisms of an unusual SAM-dependent enzyme. Signal Transduct Target Ther (2019)

Release Date

2019-05-01

Peptides

O-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

O-methyltransferase

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