2W8L

Y-family DNA polymerase Dpo4 bypassing N2-naphthyl-guanine adduct in anti orientation

Replaces:  2V4T

Summary for 2W8L

• Entry DOI: 10.2210/pdb2w8l/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 2V9W 2VA2 2VA3 2W8K
• Descriptor: DNA POLYMERASE IV, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*DOC)-3', 5'-D(*TP*CP*AP*CP*N2GP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... (6 entities in total)
• Functional Keywords: dna-directed dna polymerase, dna, dpo4, adduct, n2-alkyl, cytoplasm, magnesium, transferase, metal-binding, mutator protein, dna replication, nucleotidyltransferase, complex, polymerase, dna damage, dna repair, dna-binding, transferase/dna, transferase-dna complex
• Biological source: SULFOLOBUS SOLFATARICUS
• Cellular location: Cytoplasm (Probable): Q97W02
• Total number of polymer chains: 3
• Total formula weight: 51549.37

Authors

Eoff, R.L.,Zhang, H.,Egli, M.,Guengerich, F.P. (deposition date: 2009-01-16, release date: 2009-01-27, Last modification date: 2023-12-13)

Primary citation

Zhang, H.,Eoff, R.L.,Kozekov, I.D.,Rizzo, C.J.,Egli, M.,Guengerich, F.P.
Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts.
J.Biol.Chem., 284:3563-, 2009

PubMed Abstract: In contrast to replicative DNA polymerases, Sulfolobus solfataricus Dpo4 showed a limited decrease in catalytic efficiency (k(cat)/Km) for insertion of dCTP opposite a series of N2-alkylguanine templates of increasing size from (methyl (Me) to (9-anthracenyl)-Me (Anth)). Fidelity was maintained with increasing size up to (2-naphthyl)-Me (Naph). The catalytic efficiency increased slightly going from the N2-NaphG to the N2-AnthG substrate, at the cost of fidelity. Pre-steady-state kinetic bursts were observed for dCTP incorporation throughout the series (N2-MeG to N2-AnthG), with a decrease in the burst amplitude and k(pol), the rate of single-turnover incorporation. The pre-steady-state kinetic courses with G and all of the six N2-alkyl G adducts could be fit to a general DNA polymerase scheme to which was added an inactive complex in equilibrium with the active ternary Dpo4.DNA.dNTP complex, and only the rates of equilibrium with the inactive complex and phosphodiester bond formation were altered. Two crystal structures of Dpo4 with a template N2-NaphG (in a post-insertion register opposite a 3'-terminal C in the primer) were solved. One showed N2-NaphG in a syn conformation, with the naphthyl group located between the template and the Dpo4 "little finger" domain. The Hoogsteen face was within hydrogen bonding distance of the N4 atoms of the cytosine opposite N2-NaphG and the cytosine at the -2 position. The second structure showed N2-Naph G in an anti conformation with the primer terminus largely disordered. Collectively these results explain the versatility of Dpo4 in bypassing bulky G lesions.

PubMed: 19059910
DOI: 10.1074/JBC.M807778200

Experimental method

X-RAY DIFFRACTION (3 Å)