› 6p78

X-ray diffraction
1.73Å resolution

queuine lyase from Clostridium spiroforme bound to SAM and queuine

Released:
DOI: 10.2210/pdb6p78/pdb
PDB entry 6p78 coloured by chain, front view.
PDB entry 6p78 coloured by chain, side view.
PDB entry 6p78 coloured by chain, top view.
Source organism: [Clostridium] spiroforme DSM 1552
Primary publication:
Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens.
Yuan Y, Zallot R, Grove TL, Payan DJ, Martin-Verstraete I, Šepić S, Balamkundu S, Neelakandan R, Gadi VK, Liu CF, Swairjo MA, Dedon PC, Almo SC, Gerlt JA, de Crécy-Lagard V
Proc Natl Acad Sci U S A 116 19126-19135 (2019)
PMID: 31481610

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109291 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Elp3/MiaA/NifB-like radical SAM core domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 251 amino acids
Theoretical weight: 29.93 KDa
Source organism: [Clostridium] spiroforme DSM 1552
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B1C2R2 (Residues: 1-229; Coverage: 100%)
Gene name: CLOSPI_01524

Ligands and Environments

3 bound ligands:
Ligand SF4 1 x SF4
Ligand QUG 1 x QUG
Ligand SAM 1 x SAM
1 modified residue:
Ligand SMC 1 x SMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P43212
Unit cell:
a: 57.606Å b: 57.606Å c: 152.414Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.165 0.2
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Naturally occurring modified ribonucleosides.
McCown et al. (2020)
4 more

1 mention without citation

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens.
Yuan et al. (2019)