2W7P

Structure and Activity of Bypass Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-oxodeoxyguanosine Adduct

Summary for 2W7P

• Entry DOI: 10.2210/pdb2w7p/pdb
• Related: 1T94 2W7O
• Descriptor: DNA POLYMERASE KAPPA, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3', 5'-D(TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP*TP* TP*CP*CP*CP*CP*C)-3', ... (6 entities in total)
• Functional Keywords: 8-oxo-2p-deoxy-guanosine-5p-monophosphate, translesion dna polymerase, human dna polymerase kappa, datp, dna repair, dna damage, dna-binding protein, dna binding protein
• Biological source: HOMO SAPIENS (HUMAN)
• Cellular location: Nucleus: Q9UBT6
• Total number of polymer chains: 6
• Total formula weight: 136189.56

Authors

Irimia, A.,Egli, M. (deposition date: 2008-12-23, release date: 2009-06-16, Last modification date: 2023-12-13)

Primary citation

Irimia, A.,Eoff, R.L.,Guengerich, F.P.,Egli, M.
Structural and Functional Elucidation of the Mechanism Promoting Error-Prone Synthesis by Human DNA Polymerase Kappa Opposite the 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine Adduct.
J.Biol.Chem., 284:22467-, 2009

PubMed Abstract: Human polymerase kappa (hPol kappa) is one of four eukaryotic Y-class DNA polymerases and may be an important element in the cellular response to polycyclic aromatic hydrocarbons such as benzo[a]pyrene, which can lead to reactive oxygenated metabolite-mediated oxidative stress. Here, we present a detailed analysis of the activity and specificity of hPol kappa bypass opposite the major oxidative adduct 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG). Unlike its archaeal homolog Dpo4, hPol kappa bypasses this lesion in an error-prone fashion by inserting mainly dATP. Analysis of transient-state kinetics shows diminished "bursts" for dATP:8-oxoG and dCTP:8-oxoG incorporation, indicative of non-productive complex formation, but dATP:8-oxoG insertion events that do occur are 2-fold more efficient than dCTP:G insertion events. Crystal structures of ternary hPol kappa complexes with adducted template-primer DNA reveal non-productive (dGTP and dATP) alignments of incoming nucleotide and 8-oxoG. Structural limitations placed upon the hPol kappa by interactions between the N-clasp and finger domains combined with stabilization of the syn-oriented template 8-oxoG through the side chain of Met-135 both appear to contribute to error-prone bypass. Mutating Leu-508 in the little finger domain of hPol kappa to lysine modulates the insertion opposite 8-oxoG toward more accurate bypass, similar to previous findings with Dpo4. Our structural and activity data provide insight into important mechanistic aspects of error-prone bypass of 8-oxoG by hPol kappa compared with accurate and efficient bypass of the lesion by Dpo4 and polymerase eta.

PubMed: 19542228
DOI: 10.1074/JBC.M109.003905

Experimental method

X-RAY DIFFRACTION (3.71 Å)