SMTL ID : 5c0o.1

m1A58 tRNA methyltransferase mutant - Y78A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-tetramer

Ligands

4 x SAM: S-ADENOSYLMETHIONINE(Covalent)(Non-covalent)

SAM.1: 22 residues within 4Å: Chain A: A.74, T.75, P.76, T.77, G.101, T.102, G.103, S.104, G.105, G.106, L.107, Y.124, E.125, A.126, R.127, H.130, G.152, K.153, L.154, E.155, D.170, L.171 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.77, A:T.77, A:G.101, A:S.104, A:G.105, A:G.106, A:L.107, A:A.126, A:R.127, A:H.130, A:L.154, A:E.155 Water bridges: A:T.108 Salt bridges: A:D.170 SAM.2: 16 residues within 4Å: Chain B: T.75, P.76, T.77, G.101, T.102, G.103, G.105, G.106, L.107, E.125, A.126, R.127, H.130, K.153, D.170, L.171 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.170 Hydrogen bonds: B:G.105, B:L.107, B:R.127, B:K.153 Water bridges: B:T.75 Salt bridges: B:D.170 SAM.4: 22 residues within 4Å: Chain C: A.74, T.75, P.76, T.77, G.101, T.102, G.103, S.104, G.105, G.106, L.107, Y.124, E.125, A.126, R.127, H.130, G.152, K.153, L.154, E.155, D.170, L.171 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:T.77, C:T.77, C:T.77, C:G.101, C:S.104, C:G.105, C:G.106, C:L.107, C:A.126, C:R.127, C:L.154, C:E.155, C:D.170 Water bridges: C:T.108, C:M.172 Salt bridges: C:D.170 SAM.5: 21 residues within 4Å: Chain D: A.74, T.75, P.76, T.77, G.101, T.102, G.103, S.104, G.105, G.106, L.107, E.125, A.126, R.127, H.130, G.152, K.153, L.154, E.155, D.170, L.171 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.77, D:T.77, D:G.101, D:G.101, D:T.102, D:S.104, D:G.105, D:G.106, D:L.107, D:A.126, D:H.130, D:L.154, D:E.155 Water bridges: D:T.108 Salt bridges: D:D.170

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 8 residues within 4Å: Chain B: W.226, E.227, V.228, R.236 Chain D: L.215, E.216, R.217, V.218 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:W.226, B:V.228, D:L.215, D:V.218 Salt bridges: B:R.236

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Degut, C. et al., The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI. Biophys.Chem. (2016)

Release Date

2015-07-08

Peptides

tRNA (adenine(58)-N(1))-methyltransferase TrmI: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

tRNA (adenine(58)-N(1))-methyltransferase TrmI