3PZP

Human DNA polymerase kappa extending opposite a cis-syn thymine dimer

Summary for 3PZP

• Entry DOI: 10.2210/pdb3pzp/pdb
• Related: 1T94 2OH2 3IN5
• Descriptor: DNA polymerase kappa, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3', 5'-D(*TP*TP*CP*CP*(TTD)P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', ... (6 entities in total)
• Functional Keywords: dna nucleotidyltransferase, dna binding nucleotide binding magnesium binding, nucleus, transferase-dna complex, transferase/dna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: Q9UBT6
• Total number of polymer chains: 6
• Total formula weight: 137754.20

Authors

Vasquez-Del Carpio, R.,Silverstein, T.D.,Lone, S.,Johnson, R.E.,Prakash, S.,Prakash, L.,Aggarwal, A.K. (deposition date: 2010-12-14, release date: 2011-12-28, Last modification date: 2023-09-13)

Primary citation

Vasquez-Del Carpio, R.,Silverstein, T.D.,Lone, S.,Johnson, R.E.,Prakash, L.,Prakash, S.,Aggarwal, A.K.
Role of human DNA polymerase kappa in extension opposite from a cis-syn thymine dimer.
J.Mol.Biol., 408:252-261, 2011

PubMed Abstract: Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase κ (Polκ), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Polκ in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure reveals a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Polκ in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.

PubMed: 21354175
DOI: 10.1016/j.jmb.2011.02.042

Experimental method

X-RAY DIFFRACTION (3.336 Å)