3rh4 | pdb_00003rh4
DNA Polymerase Beta with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP)
Structural highlights
Function[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] Publication Abstract from PubMedDNA polymerases can misinsert ribonucleotides that lead to genomic instability. DNA polymerase beta discourages ribonucleotide insertion with the backbone carbonyl of Tyr-271; alanine substitution of Tyr-271, but not Phe-272, resulted in a > 10-fold loss in discrimination. The Y271A mutant also inserted ribonucleotides more efficiently than wild type on a variety of rNMP-containing DNA substrates. Substituting Mn(2+) for Mg(2+) decreased sugar discrimination for both wild-type and mutant enzymes primarily by increasing the affinity for rCTP. This facilitated crystallization of ternary substrate complexes of both the wild-type and Y271A mutant enzymes. Crystallographic structures of Y271A- and wild type-substrate complexes indicate that rCTP is well accommodated in the active site, but that O2' of rCTP and the carbonyl oxygen of Tyr-271 or Ala-271 are unusually close (~2.5 and 2.6 A, respectively). Structure-based modeling indicates that the local energetic cost of positioning these closely spaced oxygens is ~2.2 kcal/mol for the wild-type enzyme. Since the side chain of Tyr-271 also hydrogen bonds with the primer terminus, loss of this interaction affects its catalytic positioning. Our results support a model where DNA polymerase beta utilizes two strategies, steric and geometric, with a single protein residue to deter ribonucleotide insertion. Molecular insights into DNA polymerase deterrents for Ribonucleotide insertion.,Cavanaugh NA, Beard WA, Batra VK, Perera L, Pedersen LG, Wilson SH J Biol Chem. 2011 Jul 6. PMID:21733843[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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