PDBsum entry 8byh

Transferase

PDB id: 8byh

Contents

Protein chains

239 a.a.

Ligands

EDO ×5

GOL

SAM ×2

Metals

_CL ×3

Waters ×396

PDB id:

8byh

Name:

Transferase

Title:

Crystal structure of trmd domain from calditerrivibrio nitroreducens in complex with s-adenosyl-l-methionine

Structure:

tRNA (guanine-n(1)-)-methyltransferase. Chain: a, b. Engineered: yes

Source:

Calditerrivibrio nitroreducens dsm 19672. Organism_taxid: 768670. Gene: trmd. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

2.19Å R-factor: 0.169 R-free: 0.209

Authors:

A.Kluza,I.Lewandowska,J.Sulkowska

Key ref:

J.Sulkowska Are there double knots in proteins? prediction and in verification based on trmd-Tm1570 fusion from c. Nitroreducens. To be published. To be published, .

Date:

12-Dec-22 Release date: 11-Jan-23

Protein chains

E4THH1  (E4THH1_CALNY) -  tRNA (guanine-N(1)-)-methyltransferase from Calditerrivibrio nitroreducens (strain DSM 19672 / NBRC 101217 / Yu37-1)

Seq: 433 a.a.

Struc: 239 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.228 - tRNA (guanine(37)-N(1))-methyltransferase.
• Reaction: guanosine₃₇ in tRNA + S-adenosyl-L-methionine = N₁- methylguanosine₃₇ in tRNA + S-adenosyl-L-homocysteine + H⁺

guanosine(37) in tRNA + S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = N(1)- methylguanosine(37) in tRNA + S-adenosyl-L-homocysteine + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site