SMTL ID : 6jki.1

Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-dimer

Ligands

2 x SFG: SINEFUNGIN(Non-covalent)(Covalent)

SFG.1: 25 residues within 4Å: Chain A: Y.89, L.90, S.91, P.92, Q.93, G.116, R.117, Y.118, E.119, G.120, W.134, S.135, I.136, G.137, Y.139, V.140, L.141, S.142, G.143, G.144, P.147 Chain B: D.172, S.173, D.180 Ligands: MN.18 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:V.140 Hydrogen bonds: A:Y.89, A:Q.93, A:G.116, A:Y.118, A:I.136, A:Y.139, A:L.141, B:S.173, B:D.180, B:D.180 Water bridges: A:Y.89, A:S.91, B:R.157 SFG.6: 23 residues within 4Å: Chain A: S.173, D.180 Chain B: Y.89, L.90, S.91, P.92, Q.93, G.116, Y.118, E.119, G.120, W.134, S.135, I.136, G.137, Y.139, V.140, L.141, S.142, G.143, G.144, P.147 Ligands: MN.7 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.140 Hydrogen bonds: B:Y.89, B:G.116, B:Y.118, B:I.136, B:Y.139, B:L.141, A:S.173, A:S.173, A:D.180, A:D.180 Water bridges: B:Y.89, B:Q.93, A:R.157, A:R.157

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: P.12, S.19, L.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.19 Water bridges: A:L.35 GOL.3: 10 residues within 4Å: Chain A: Y.89, Q.93, E.119, G.120, I.121, E.123, I.126 Chain B: C.181, P.182, H.183 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:C.181, B:H.183, B:H.183, A:Y.89, A:Y.89, A:Q.93, A:I.121, A:E.123 Water bridges: A:S.91 GOL.4: 3 residues within 4Å: Chain A: V.28, K.29, G.31 No protein-ligand interaction detected (PLIP) GOL.5: 4 residues within 4Å: Chain A: E.171, D.172 Chain B: P.60, E.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.171, A:D.172 GOL.11: 6 residues within 4Å: Chain B: P.12, F.15, R.16, S.19, L.35, C.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.15, B:S.19, B:L.35 GOL.12: 2 residues within 4Å: Chain B: V.42, D.75 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.42, B:D.75 GOL.13: 4 residues within 4Å: Chain B: R.41, T.44, R.47, Q.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.41, B:R.41, B:T.44 GOL.15: 3 residues within 4Å: Chain B: E.221, Y.243, R.247 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.247 GOL.16: 4 residues within 4Å: Chain B: G.71, A.74, D.75, Q.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.71 GOL.17: 3 residues within 4Å: Chain B: G.234, E.235, K.238 No protein-ligand interaction detected (PLIP)

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.7: 5 residues within 4Å: Chain A: E.171, D.172, D.180 Chain B: E.119 Ligands: SFG.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.171, H2O.3 MN.8: 3 residues within 4Å: Chain A: E.127 Chain B: Y.184, R.194 No protein-ligand interaction detected (PLIP) MN.18: 6 residues within 4Å: Chain A: E.119 Chain B: E.171, D.172, D.180, H.183 Ligands: SFG.1 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.171, B:D.180

2 x NA: SODIUM ION(Non-functional Binders)

NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.19: 1 residues within 4Å: Chain B: R.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.186

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 13 residues within 4Å: Chain A: A.17, I.18, Y.21, I.23, T.24, D.153 Chain B: M.14, R.117, S.142, G.143, E.145, L.146, P.147 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.117, B:R.117, B:S.142, B:G.143, B:G.143, B:E.145, B:L.146, A:Y.21, A:I.23, A:T.24, A:D.153 PEG.14: 5 residues within 4Å: Chain B: D.172, T.175, L.179, D.180, L.212 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jaroensuk, J. et al., Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa. Rna (2019)

Release Date

2019-07-03

Peptides

tRNA (guanine-N(1)-)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA (guanine-N(1)-)-methyltransferase