SMTL ID : 6jpl.2 (1 other biounit)

The X-ray structure of yeast tRNA methyltransferase Trm7-Trm734 in complex with S-adenosyl-L-methionine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-1-1-mer

Ligands

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.1: 6 residues within 4Å: Chain A: F.520, V.521, F.576, G.580, K.745, R.746 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.521 Salt bridges: A:K.745, A:R.746

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

SO4.2: 7 residues within 4Å: Chain A: D.3, H.6, R.43, T.978, T.979, S.1009, W.1011 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.978, A:T.979, A:S.1009, A:W.1011 Water bridges: A:R.43, A:R.43 Salt bridges: A:H.6, A:R.43 SO4.3: 2 residues within 4Å: Chain A: N.577, S.578 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.578, A:S.578 Salt bridges: A:K.619 SO4.4: 5 residues within 4Å: Chain A: I.945, N.946, G.947, S.990, K.999 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.946, A:G.947, A:S.990 Salt bridges: A:K.999 SO4.5: 3 residues within 4Å: Chain A: N.90, S.91, R.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.90, A:S.91, A:S.91 Water bridges: A:N.90 Salt bridges: A:R.127 SO4.6: 4 residues within 4Å: Chain A: G.609, S.611, K.630, A.631 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.611, A:A.631 Salt bridges: A:R.613

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

SAM.7: 18 residues within 4Å: Chain B: S.25, C.51, A.52, A.53, P.54, G.55, S.56, W.57, D.83, L.84, Q.85, A.98, D.99, I.100, D.124, G.125, A.126, L.143 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:S.25, B:C.51, B:A.53, B:G.55, B:S.56, B:W.57, B:L.84, B:Q.85, B:Q.85, B:D.99, B:I.100, B:D.124, B:D.124, B:D.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirata, A. et al., Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition. Nucleic Acids Res. (2019)

Release Date

2019-10-02

Peptides

tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734: A
tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

tRNA (guanosine(34)-2'-O)-methyltransferase non-catalytic subunit TRM734

tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase

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