› 4jwj

X-ray diffraction
1.76Å resolution

Crystal structure of scTrm10(84)-SAH complex

Released:
DOI: 10.2210/pdb4jwj/pdb
PDB entry 4jwj coloured by chain, front view.
PDB entry 4jwj coloured by chain, side view.
PDB entry 4jwj coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate.
Shao Z, Yan W, Peng J, Zuo X, Zou Y, Li F, Gong D, Ma R, Wu J, Shi Y, Zhang Z, Teng M, Li X, Gong Q
OpenAccess logo Nucleic Acids Res 42 509-25 (2014)
PMID: 24081582

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + guanine(9) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(9) in tRNA
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171353 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (guanine(9)-N1)-methyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 202 amino acids
Theoretical weight: 23.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12400 (Residues: 84-276; Coverage: 66%)
Gene names: O0926, TRM10, YOL093W
Sequence domains: tRNA (Guanine-1)-methyltransferase
Structure domains: Alpha/beta knot

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
2 bound ligands:
Ligand SO4 4 x SO4
Ligand TRS 3 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 131.583Å b: 58.861Å c: 99.767Å
α: 90° β: 131.13° γ: 90°
R-values:
R R work R free
0.24 0.218 0.251
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Modifications and functional genomics of human transfer RNA.
Pan T. (2018)
9 more

8 mentions without citation

m1A Post-Transcriptional Modification in tRNAs.
Oerum et al. (2017)
7 more