2LJ6

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

Summary for 2LJ6

• Entry DOI: 10.2210/pdb2lj6/pdb
• NMR Information: BMRB: 17283
• Descriptor: Probable ATP-dependent DNA ligase (1 entity in total)
• Functional Keywords: phosphoesterase, dna binding protein
• Biological source: Pseudomonas aeruginosa
• Total number of polymer chains: 1
• Total formula weight: 20257.94

Authors

Dutta, K.,Natarajan, A.,Shuman, S.,Ghose, R. (deposition date: 2011-09-06, release date: 2011-11-16, Last modification date: 2024-05-15)

Primary citation

Natarajan, A.,Dutta, K.,Temel, D.B.,Nair, P.A.,Shuman, S.,Ghose, R.
Solution structure and DNA-binding properties of the phosphoesterase domain of DNA ligase D.
Nucleic Acids Res., 40:2076-2088, 2012

PubMed Abstract: 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+).

PubMed: 22084199
DOI: 10.1093/nar/gkr950

Experimental method

SOLUTION NMR