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4m9n, resolution 2.27Å ()
Ligands: , ,
Related: 4m9g, 4m9h, 4m9j, 4m9l

Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


DNA Polymerase Beta E295K Soaked with dATP

Publication Abstract from PubMed

DNA polymerase beta (pol beta) is responsible for gap filling synthesis during repair of damaged DNA as part of the base excision repair pathway. Human pol beta mutations were recently identified in a high percentage (~30%) of tumors. Characterization of specific cancer variants is particularly useful to further the understanding of the general mechanism of pol beta while providing context to disease contribution. We showed that expression of the carcinoma variant E295K induces cellular transformation. The poor polymerase activity exhibited by the variant was hypothesized to be caused by the destabilization of proper active site assembly by the glutamate to lysine mutation. Here we show that this variant exhibits an unusual preference for binding dCTP opposite a templating adenine over the cognate dTTP. Biochemical studies indicate that the non-cognate competes with the cognate nucleotide for binding to the polymerase active site with the non-cognate incorporation a function of higher affinity and not increased activity. In the crystal structure of the variant bound to dA:dCTP, the fingers domain closes around the mismatched base pair. Nucleotide incorporation is hindered because key residues in the polymerase active site are not properly positioned for nucleotidyl transfer. In contrast to the non-cognate dCTP, neither the cognate dTTP nor its non-hydrolyzable analog induced fingers closure, as isomorphous difference Fourier maps show that the cognate nucleotides are bound to the open state of the polymerase. Comparison to published structures provides insight into the structural rearrangements within pol beta that occur during the process of nucleotide discrimination.

The E295K cancer variant of human polymerase beta favors the mismatch conformational pathway during nucleotide selection., Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S, J Biol Chem. 2013 Oct 18. PMID:24133209

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.


[DPOLB_HUMAN] Repair polymerase that plays a key role in base-excision repair. Has 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity that removes the 5' sugar phosphate and also acts as a DNA polymerase that adds one nucleotide to the 3' end of the arising single-nucleotide gap. Conducts 'gap-filling' DNA synthesis in a stepwise distributive fashion rather than in a processive fashion as for other DNA polymerases.[1] [2] [3] [4]

About this Structure

4m9n is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA.


  • Eckenroth BE, Towle-Weicksel JB, Sweasy JB, Doublie S. The E295K cancer variant of human polymerase beta favors the mismatch conformational pathway during nucleotide selection. J Biol Chem. 2013 Oct 18. PMID:24133209 doi:http://dx.doi.org/10.1074/jbc.M113.510891
  1. Bennett RA, Wilson DM 3rd, Wong D, Demple B. Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7166-9. PMID:9207062
  2. Matsumoto Y, Kim K, Katz DS, Feng JA. Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups. Biochemistry. 1998 May 5;37(18):6456-64. PMID:9572863 doi:10.1021/bi9727545
  3. DeMott MS, Beyret E, Wong D, Bales BC, Hwang JT, Greenberg MM, Demple B. Covalent trapping of human DNA polymerase beta by the oxidative DNA lesion 2-deoxyribonolactone. J Biol Chem. 2002 Mar 8;277(10):7637-40. Epub 2002 Jan 22. PMID:11805079 doi:10.1074/jbc.C100577200
  4. Parsons JL, Dianova II, Khoronenkova SV, Edelmann MJ, Kessler BM, Dianov GL. USP47 is a deubiquitylating enzyme that regulates base excision repair by controlling steady-state levels of DNA polymerase beta. Mol Cell. 2011 Mar 4;41(5):609-15. doi: 10.1016/j.molcel.2011.02.016. PMID:21362556 doi:10.1016/j.molcel.2011.02.016

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