2C2D

Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

Summary for 2C2D

• Entry DOI: 10.2210/pdb2c2d/pdb
• Related: 1JX4 1JXL 1N48 1N56 1RYR 1RYS 1S0M 1S0N 1S0O 1S10 1S97 1S9F 2AGO 2AGP 2AGQ 2BQ3 2BQR 2BQU 2BR0 2C22 2C28 2C2E 2C2R
• Descriptor: DNA POLYMERASE IV, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3', 5'-D(*TP*CP*AP*C 8OGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... (6 entities in total)
• Functional Keywords: polymerase, p2 dna polymerase iv, 8-oxo-2p-deoxy-guanosine-5p- monophosphate, translesion dna polymerase, datp, nucleotidyltransferase, transferase, dna damage, dna repair, dna replication, dna-binding, dna-directed dna polymerase, metal-binding, mutator protein, magnesium
• Biological source: SULFOLOBUS SOLFATARICUS; More
• Cellular location: Cytoplasm : Q97W02
• Total number of polymer chains: 3
• Total formula weight: 51754.66

Authors

Irimia, A.,Loukachevitch, L.V.,Egli, M. (deposition date: 2005-09-27, release date: 2005-11-29, Last modification date: 2023-12-13)

Primary citation

Zang, H.,Irimia, A.,Choi, J.-Y.,Angel, K.C.,Loukachevitch, L.V.,Egli, M.,P Guengerich, F.
Efficient and High Fidelity Incorporation of Dctp Opposite 7,8-Dihydro-8-Oxodeoxyguanosine by Sulfolobus Solfataricus DNA Polymerase Dpo4
J.Biol.Chem., 281:2358-, 2006

PubMed Abstract: DNA polymerases insert dATP opposite the oxidative damage product 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) instead of dCTP, to the extent of >90% with some polymerases. Steady-state kinetics with the Y-family Sulfolobus solfataricus DNA polymerase IV (Dpo4) showed 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) was similar for G and 8-oxoG templates. Mass spectral analysis of extended DNA primers showed >/=95% incorporation of dCTP > dATP opposite 8-oxoG. Pre-steady-state kinetics showed faster rates of dCTP incorporation opposite 8-oxoG than G. The measured K(d)(,dCTP) was 15-fold lower for an oligonucleotide containing 8-oxoG than with G. Extension beyond an 8-oxoG:C pair was similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. The E(a) for dCTP insertion opposite 8-oxoG was lower than for opposite G. Crystal structures of Dpo4 complexes with oligonucleotides were solved with C, A, and G nucleoside triphosphates placed opposite 8-oxoG. With ddCTP, dCTP, and dATP the phosphodiester bonds were formed even in the presence of Ca(2+). The 8-oxoG:C pair showed classic Watson-Crick geometry; the 8-oxoG:A pair was in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5' C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshift event observed in the catalytic assays.

PubMed: 16306039
DOI: 10.1074/JBC.M510889200

Experimental method

X-RAY DIFFRACTION (2.57 Å)