3U7E

Crystal structure of mPNKP catalytic fragment (D170A)

Summary for 3U7E

• Entry DOI: 10.2210/pdb3u7e/pdb
• Related: 1YJ5
• Descriptor: Bifunctional polynucleotide phosphatase/kinase, PHOSPHATE ION, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: protein-dna complex, had family, pnkp, dna repair, phosphatase, hydrolase, transferase
• Biological source: Mus musculus (mouse)
• Cellular location: Nucleus : Q9JLV6
• Total number of polymer chains: 1
• Total formula weight: 42958.44

Authors

Coquelle, N.,Havali, Z.,Bernstein, N.,Green, R.,Glover, J.N.M. (deposition date: 2011-10-13, release date: 2011-12-14, Last modification date: 2023-12-06)

Primary citation

Coquelle, N.,Havali-Shahriari, Z.,Bernstein, N.,Green, R.,Glover, J.N.
Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates.
Proc.Natl.Acad.Sci.USA, 108:21022-21027, 2011

PubMed Abstract: Polynucleotide kinase/phosphatase (PNKP) is a critical mammalian DNA repair enzyme that generates 5'-phosphate and 3'-hydroxyl groups at damaged DNA termini that are required for subsequent processing by DNA ligases and polymerases. The PNKP phosphatase domain recognizes 3'-phosphate termini within DNA nicks, gaps, or at double- or single-strand breaks. Here we present a mechanistic rationale for the recognition of damaged DNA termini by the PNKP phosphatase domain. The crystal structures of PNKP bound to single-stranded DNA substrates reveals a narrow active site cleft that accommodates a single-stranded substrate in a sequence-independent manner. Biochemical studies suggest that the terminal base pairs of double-stranded substrates near the 3'-phosphate are destabilized by PNKP to allow substrate access to the active site. A positively charged surface distinct from the active site specifically facilitates interactions with double-stranded substrates, providing a complex DNA binding surface that enables the recognition of diverse substrates.

PubMed: 22171004
DOI: 10.1073/pnas.1112036108

Experimental method

X-RAY DIFFRACTION (1.7 Å)