› 8i6b

X-ray diffraction
1.6Å resolution

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with 5-Hydroxy-2,4(1H,3H)-pyrimidinedione, Form I

Released:
DOI: 10.2210/pdb8i6b/pdb
PDB entry 8i6b coloured by chain, front view.
PDB entry 8i6b coloured by chain, side view.
PDB entry 8i6b coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Crystal structures of non-uracil ring fragments in complex with Mycobacterium tuberculosis uracil DNA glycosylase (MtUng) as a starting point for novel inhibitor design: A case study with the barbituric acid fragment.
Kesharwani S, Raj P, Paul A, Roy K, Bhanot A, Mehta A, Gopal A, Varshney U, Gopal B, Sundriyal S
Eur J Med Chem 258 115604 (2023)
PMID: 37399710

Function and Biology Details

Reaction catalysed: 
Hydrolyzes single-stranded DNA or mismatched double-stranded DNA and polynucleotides, releasing free uracil
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161423 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uracil-DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 238 amino acids
Theoretical weight: 25.81 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WFQ9 (Residues: 1-227; Coverage: 100%)
Gene names: MTCY349.11, Rv2976c, ung
Sequence domains: Uracil DNA glycosylase superfamily

Ligands and Environments

5 bound ligands:
Ligand ODF 1 x ODF
Ligand EDO 1 x EDO
Ligand DMS 5 x DMS
Ligand NA 1 x NA
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BRUKER AXS MICROSTAR
Spacegroup: P21
Unit cell:
a: 39.16Å b: 63.68Å c: 45.19Å
α: 90° β: 112.58° γ: 90°
R-values:
R R work R free
0.151 0.149 0.182
Expression system: Escherichia coli BL21(DE3)

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