2LJ6: Solution Structure and DNA-binding Properties of the Phosphoesterase Domain of DNA Ligase D

The phosphoesterase (PE) domain of the bacterial DNA repair enzyme LigD possesses distinctive manganese-dependent 3'-phosphomonoesterase and 3'-phosphodiesterase activities. PE exemplifies a new family of DNA end-healing enzymes found in all phylogenetic domains. Here, we determined the structure of the PE domain of Pseudomonas aeruginosa LigD (PaePE) using solution NMR methodology. PaePE has a disordered N-terminus and a well-folded core that differs in instructive ways from the crystal structure of a PaePE*Mn(2+)* sulfate complex, especially at the active site that is found to be conformationally dynamic. Chemical shift perturbations in the presence of primer-template duplexes with 3'-deoxynucleotide, 3'-deoxynucleotide 3'-phosphate, or 3' ribonucleotide termini reveal the surface used by PaePE to bind substrate DNA and suggest a more efficient engagement in the presence of a 3'-ribonucleotide. Spectral perturbations measured in the presence of weakly catalytic (Cd(2+)) and inhibitory (Zn(2+)) metals provide evidence for significant conformational changes at and near the active site, compared to the relatively modest changes elicited by Mn(2+).
PDB ID: 2LJ6Download
MMDB ID: 94994
PDB Deposition Date: 2011/9/6
Updated in MMDB: 2011/11
Experimental Method:
solution nmr
Source Organism:
Similar Structures:
Biological Unit for 2LJ6: monomeric; determined by author
Molecular Components in 2LJ6
Label Count Molecule
Protein (1 molecule)
Probable Atp-dependent DNA Ligase(Gene symbol: PA2138)
Molecule annotation
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Citing MMDB