2W9C

Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dTTP

Summary for 2W9C

• Entry DOI: 10.2210/pdb2w9c/pdb
• Related: 1JX4 1JXL 1N48 1N56 1RYR 1RYS 1S0M 1S0N 1S0O 1S10 1S97 1S9F 2AGO 2AGP 2AGQ 2ASD 2ASJ 2ASL 2ATL 2AU0 2BQ3 2BQR 2BQU 2BR0 2C22 2C28 2C2D 2C2E 2C2R 2J6S 2J6T 2J6U 2JEF 2JEG 2JEI 2JEJ 2UVR 2UVU 2UVV 2UVW 2V4Q 2V4R 2V4S 2V4T 2V9W 2VA2 2VA3 2W8K 2W8L 2W9A 2W9B
• Descriptor: DNA POLYMERASE IV, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*DOCP)-3', 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... (7 entities in total)
• Functional Keywords: dna-directed dna polymerase, n2-dimethyl-g, metal-binding, mutator protein, dna damage, dna repair, dna-binding, transferase, dna replication, nucleotidyltransferase, transferase/dna, dna, dpo4, adduct, cytoplasm, magnesium, polymerase, transferase-dna complex
• Biological source: SULFOLOBUS SOLFATARICUS; More
• Cellular location: Cytoplasm (Probable): Q97W02 2W9C
• Total number of polymer chains: 6
• Total formula weight: 102274.10

Authors

Eoff, R.L.,Zhang, H.,Kosekov, I.D.,Rizzo, C.J.,Egli, M.,Guengerich, F.P. (deposition date: 2009-01-22, release date: 2009-05-12, Last modification date: 2023-12-13)

Primary citation

Zhang, H.,Eoff, R.L.,Kosekov, I.D.,Rizzo, C.J.,Egli, M.,Guengerich, F.P.
Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes.
J.Biol.Chem., 284:17687-, 2009

PubMed Abstract: Previous work has shown that Y-family DNA polymerases tolerate large DNA adducts, but a substantial decrease in catalytic efficiency and fidelity occurs during bypass of N2,N2-dimethyl (Me2)-substituted guanine (N2,N2-Me2G), in contrast to a single methyl substitution. Therefore, it is unclear why the addition of two methyl groups is so disruptive. The presence of N2,N2-Me2G lowered the catalytic efficiency of the model enzyme Sulfolobus solfataricus Dpo4 16,000-fold. Dpo4 inserted dNTPs almost at random during bypass of N2,N2-Me2G, and much of the enzyme was kinetically trapped by an inactive ternary complex when N2,N2-Me2G was present, as judged by a reduced burst amplitude (5% of total enzyme) and kinetic modeling. One crystal structure of Dpo4 with a primer having a 3'-terminal dideoxycytosine (Cdd) opposite template N2,N2-Me2G in a post-insertion position showed Cdd folded back into the minor groove, as a catalytically incompetent complex. A second crystal had two unique orientations for the primer terminal Cdd as follows: (i) flipped into the minor groove and (ii) a long pairing with N2,N2-Me2G in which one hydrogen bond exists between the O-2 atom of Cdd and the N-1 atom of N2,N2-Me2G, with a second water-mediated hydrogen bond between the N-3 atom of Cdd and the O-6 atom of N2,N2-Me2G. A crystal structure of Dpo4 with dTTP opposite template N2,N2-Me2G revealed a wobble orientation. Collectively, these results explain, in a detailed manner, the basis for the reduced efficiency and fidelity of Dpo4-catalyzed bypass of N2,N2-Me2G compared with mono-substituted N2-alkyl G adducts.

PubMed: 19542237
DOI: 10.1074/JBC.M109014274

Experimental method

X-RAY DIFFRACTION (2.9 Å)