› 1mxi

X-ray diffraction
1.7Å resolution

Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a Cofactor Bound at a Site Formed by a Knot

Released:
DOI: 10.2210/pdb1mxi/pdb
PDB entry 1mxi coloured by chain, front view.
PDB entry 1mxi coloured by chain, side view.
PDB entry 1mxi coloured by chain, top view.
Source organism: Haemophilus influenzae
Primary publication:
Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot.
Lim K, Zhang H, Tempczyk A, Krajewski W, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O
Proteins 51 56-67 (2003)
PMID: 12596263

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine(34) in tRNA(Leu) = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine(34) in tRNA(Leu)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155219 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (cytidine(34)-2'-O)-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 160 amino acids
Theoretical weight: 18.43 KDa
Source organism: Haemophilus influenzae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P44868 (Residues: 1-160; Coverage: 100%)
Gene names: HI_0766, trmL
Sequence domains: SpoU rRNA Methylase family
Structure domains: Alpha/beta knot

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
1 bound ligand:
Ligand IOD 1 x IOD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P41212
Unit cell:
a: 40.8Å b: 40.8Å c: 165.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.196 0.254
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Methylated nucleosides in tRNA and tRNA methyltransferases.
Hori H. (2014)
9 more

17 mentions without citation

Many paths to methyltransfer: a chronicle of convergence.
Schubert et al. (2003)
16 more