› 4lgt

X-ray diffraction
1.3Å resolution

Crystal structure of the catalytic domain of RluB in complex with a 21-nucleotide RNA substrate

Released:
DOI: 10.2210/pdb4lgt/pdb
PDB entry 4lgt coloured by chain, front view.
PDB entry 4lgt coloured by chain, side view.
PDB entry 4lgt coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs.
Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM
Nucleic Acids Res 42 2037-48 (2014)
PMID: 24214967

Function and Biology Details

Reaction catalysed: 
23S rRNA uridine(2605) = 23S rRNA pseudouridine(2605)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153483 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Ribosomal large subunit pseudouridine synthase B Chains: A, D
Molecule details ›
Chains: A, D
Length: 255 amino acids
Theoretical weight: 28.6 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P37765 (Residues: 1-251; Coverage: 86%)
Gene names: JW1261, b1269, rluB, yciL
Sequence domains:
Structure domains:
stem-loop of 23S rRNA Chains: E, F
Molecule details ›
Chains: E, F
Length: 21 nucleotides
Theoretical weight: 6.83 KDa
Source organism: Escherichia coli K-12
Expression system: Not provided

Ligands and Environments

No bound ligands
2 modified residues:
Ligand OCS 2 x OCS
Ligand FHU 2 x FHU

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2
Unit cell:
a: 80.94Å b: 42.2Å c: 169.43Å
α: 90° β: 102.61° γ: 90°
R-values:
R R work R free
0.174 0.173 0.203
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Pseudouridine: still mysterious, but never a fake (uridine)!
Spenkuch et al. (2014)
2 more

3 mentions without citation

Pi-Pi contacts are an overlooked protein feature relevant to phase separation.
Vernon et al. (2018)
2 more