› 4kdz

X-ray diffraction
2.32Å resolution

Crystal structure of tRNA/rRNA methyltransferase YibK from Escherichia coli (Target NYSGRC-012599)

Released:
DOI: 10.2210/pdb4kdz/pdb
PDB entry 4kdz coloured by chain, front view.
PDB entry 4kdz coloured by chain, side view.
PDB entry 4kdz coloured by chain, top view.
Source organism: Escherichia coli UTI89
Entry authors: Kim J, Toro R, Bhosle R, Almo SC, New York Structural Genomics Research Consortium (NYSGRC)

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-173038 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (cytidine(34)-2'-O)-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 157 amino acids
Theoretical weight: 17.75 KDa
Source organism: Escherichia coli UTI89
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q1R4Y9 (Residues: 1-157; Coverage: 100%)
Gene names: UTI89_C4147, trmL, yibK
Sequence domains: SpoU rRNA Methylase family
Structure domains: Alpha/beta knot

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P3221
Unit cell:
a: 84.435Å b: 84.435Å c: 78.654Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.185 0.226
Expression system: Escherichia coli BL21(DE3)

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