› 4pum

X-ray diffraction
1.93Å resolution

tRNA-Guanine Transglycosylase (TGT) Mutant D156N in Complex with 6-Amino-2-(methylamino)-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one

Released:
DOI: 10.2210/pdb4pum/pdb
PDB entry 4pum coloured by chain, front view.
PDB entry 4pum coloured by chain, side view.
PDB entry 4pum coloured by chain, top view.
Source organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Primary publication:
Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme.
Neeb M, Czodrowski P, Heine A, Barandun LJ, Hohn C, Diederich F, Klebe G
J Med Chem 57 5554-65 (2014)
PMID: 24955548

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 analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151274 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Queuine tRNA-ribosyltransferase Chain: A
Molecule details ›
Chain: A
Length: 388 amino acids
Theoretical weight: 43.07 KDa
Source organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P28720 (Residues: 1-386; Coverage: 100%)
Gene names: ZMO0363, tgt
Sequence domains: Queuine tRNA-ribosyltransferase
Structure domains: Queuine tRNA-ribosyltransferase-like

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand GOL 2 x GOL
Ligand 2WU 1 x 2WU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: C2
Unit cell:
a: 89.69Å b: 64.66Å c: 70.77Å
α: 90° β: 93.08° γ: 90°
R-values:
R R work R free
0.161 0.159 0.202
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Molecular recognition in chemical and biological systems.
Persch et al. (2015)
3 more