› 4hug

X-ray diffraction
1.64Å resolution

Structure of 5-chlorouracil modified A:U base pairs

Released:
DOI: 10.2210/pdb4hug/pdb
PDB entry 4hug coloured by chain, front view.
PDB entry 4hug coloured by chain, side view.
PDB entry 4hug coloured by chain, top view.
Source organism: Halalkalibacterium halodurans C-125
Primary publication:
Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.
Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M
Nucleic Acids Res 41 2689-97 (2013)
PMID: 23275540

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117616 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Ribonuclease H Chains: A, B
Molecule details ›
Chains: A, B
Length: 134 amino acids
Theoretical weight: 15.43 KDa
Source organism: Alkalihalobacillus halodurans C-125
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9KEI9 (Residues: 61-194; Coverage: 68%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*CP*GP*CP*GP*AP*AP*(UCL)P*(UCL)P*CP*GP*CP*G)-3') Chains: C, D, E, F
Molecule details ›
Chains: C, D, E, F
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Halalkalibacterium halodurans C-125
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand GOL 2 x GOL
Ligand EDO 2 x EDO
1 modified residue:
Ligand UCL 8 x UCL

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P212121
Unit cell:
a: 63.829Å b: 64.638Å c: 116.286Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.193 0.222
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 citation in other articles

The 5-chlorouracil:7-deazaadenine base pair as an alternative to the dT:dA base pair.
Eremeeva et al. (2016)
2 more

3 mentions without citation

Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.
Opron et al. (2016)
2 more