2V4R

Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine

Summary for 2V4R

• Entry DOI: 10.2210/pdb2v4r/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 2V4S 2V4T 2V9W 2VA2 2VA3
• 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*CP*M1GP*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-binding, metal-binding, dna replication, mutator protein, nucleotidyltransferase, dna adduct, dna damage, dna repair, transferase, dpo4, m1dg, cytoplasm, magnesium
• Biological source: SULFOLOBUS SOLFATARICUS; More
• Total number of polymer chains: 3
• Total formula weight: 51219.35

Authors

Eoff, R.L.,Stafford, J.B.,Szekely, J.,Rizzo, C.J.,Egli, M.,Guengerich, F.P.,Marnett, L.J. (deposition date: 2008-09-26, release date: 2009-06-16, Last modification date: 2023-12-13)

Primary citation

Eoff, R.L.,Stafford, J.B.,Szekely, J.,Rizzo, C.J.,Egli, M.,Guengerich, F.P.,Marnett, L.J.
Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the Malondialdehyde-Deoxyguanosine Adduct.
Biochemistry, 48:7079-, 2009

PubMed Abstract: Oxidative stress can induce the formation of reactive electrophiles, such as DNA peroxidation products, e.g., base propenals, and lipid peroxidation products, e.g., malondialdehyde. Base propenals and malondialdehyde react with DNA to form adducts, including 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-alpha]purin-10(3H)-one (M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG (N2-OPdG). Previous work has shown that M1dG is mutagenic in bacteria and mammalian cells and that its mutagenicity in Escherichia coli is dependent on induction of the SOS response, indicating a role for translesion DNA polymerases in the bypass of M1dG. To probe the mechanism by which translesion polymerases bypass M1dG, kinetic and structural studies were conducted with a model Y-family DNA polymerase, Dpo4 from Sulfolobus solfataricus. The level of steady-state incorporation of dNTPs opposite M1dG was reduced 260-2900-fold and exhibited a preference for dATP incorporation. Liquid chromatography-tandem mass spectrometry analysis of the full-length extension products revealed a spectrum of products arising principally by incorporation of dC or dA opposite M1dG followed by partial or full-length extension. A greater proportion of -1 deletions were observed when dT was positioned 5' of M1dG. Two crystal structures were determined, including a "type II" frameshift deletion complex and another complex with Dpo4 bound to a dC.M1dG pair located in the postinsertion context. Importantly, M1dG was in the ring-closed state in both structures, and in the structure with dC opposite M1dG, the dC residue moved out of the Dpo4 active site, into the minor groove. The results are consistent with the reported mutagenicity of M1dG and illustrate how the lesion may affect replication events.

PubMed: 19492857
DOI: 10.1021/BI9003588

Experimental method

X-RAY DIFFRACTION (2.5 Å)