SMTL ID : 2yvl.1

Crystal structure of tRNA (m1A58) methyltransferase TrmI from Aquifex aeolicus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

SAM.1: 22 residues within 4Å: Chain A: T.72, Q.73, I.74, I.75, G.99, T.100, G.101, S.102, G.103, A.104, L.105, F.119, E.120, A.121, V.122, F.125, V.147, D.148, F.149, D.165, V.166, Y.172 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:I.75, A:G.99, A:G.99, A:T.100, A:G.101, A:S.102, A:G.103, A:A.104, A:L.105, A:A.121, A:F.149, A:D.165, A:Y.172 Water bridges: A:L.106, A:Y.172 Salt bridges: A:D.165 SAM.2: 22 residues within 4Å: Chain B: T.72, Q.73, I.74, I.75, G.99, T.100, G.101, S.102, G.103, A.104, L.105, F.119, E.120, A.121, V.122, F.125, V.147, D.148, F.149, D.165, V.166, Y.172 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:I.75, B:G.99, B:G.99, B:T.100, B:G.101, B:S.102, B:G.103, B:A.104, B:L.105, B:A.121, B:D.148, B:D.148, B:F.149, B:D.165 Water bridges: B:L.106 Salt bridges: B:D.165 SAM.3: 22 residues within 4Å: Chain C: T.72, Q.73, I.74, I.75, G.99, T.100, G.101, S.102, G.103, A.104, L.105, F.119, E.120, A.121, V.122, F.125, V.147, D.148, F.149, D.165, V.166, Y.172 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:I.75, C:G.99, C:G.99, C:T.100, C:S.102, C:G.103, C:A.104, C:L.105, C:A.121, C:F.149, C:Y.172 Water bridges: C:E.97, C:L.106, C:R.167 Salt bridges: C:D.165 SAM.4: 22 residues within 4Å: Chain D: T.72, Q.73, I.74, I.75, G.99, T.100, G.101, S.102, G.103, A.104, L.105, F.119, E.120, A.121, V.122, F.125, V.147, D.148, F.149, D.165, V.166, Y.172 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:I.75, D:E.97, D:E.97, D:G.99, D:T.100, D:G.101, D:S.102, D:G.103, D:A.104, D:L.105, D:A.121, D:D.148, D:F.149 Water bridges: D:L.106, D:R.167 Salt bridges: D:D.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuratani, M. et al., Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine. J Struct Funct Genomics (2014)

Release Date

2008-04-01

Peptides

Hypothetical protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypothetical protein