› 1q2s

X-ray diffraction
3.2Å resolution

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

Released:
DOI: 10.2210/pdb1q2s/pdb
PDB entry 1q2s coloured by chain, front view.
PDB entry 1q2s coloured by chain, side view.
PDB entry 1q2s coloured by chain, top view.
Source organisms:
Primary publication:
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate.
Xie W, Liu X, Huang RH
Nat Struct Biol 10 781-8 (2003)
PMID: 12949492

Function and Biology Details

Reaction catalysed: 
Guanine(34) in tRNA + 7-aminomethyl-7-carbaguanine = 7-aminomethyl-7-carbaguanine(34) in tRNA + guanine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-219357 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Queuine tRNA-ribosyltransferase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 386 amino acids
Theoretical weight: 42.93 KDa
Source organism: Zymomonas mobilis
Expression system: Escherichia coli
UniProt:
  • Canonical: P28720 (Residues: 1-386; Coverage: 100%)
Gene names: ZMO0363, tgt
Sequence domains: Queuine tRNA-ribosyltransferase
Structure domains: Queuine tRNA-ribosyltransferase-like
5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(PQ1)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3' Chain: E
Molecule details ›
Chain: E
Length: 20 nucleotides
Theoretical weight: 6.45 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3') Chain: F
Molecule details ›
Chain: F
Length: 20 nucleotides
Theoretical weight: 6.27 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand 9DG 1 x 9DG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: I4
Unit cell:
a: 261.961Å b: 261.961Å c: 55.549Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.18 0.235
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Evolution of cytokinin biosynthesis and degradation.
Frébort et al. (2011)
11 more

3 mentions without citation

A nonredundant structure dataset for benchmarking protein-RNA computational docking.
Huang et al. (2013)
2 more