2UVW

Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs

Summary for 2UVW

• Entry DOI: 10.2210/pdb2uvw/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
• Descriptor: DNA POLYMERASE IV, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-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: transferase, dna-directed dna polymerase, p2 dna polymerase iv, nucleotidyltransferase, 7, magnesium, dna damage, dna repair, dna-binding, translesion dna polymerase, metal-binding, 8-dihydro-8- oxodeoxyguanosine, metal- binding, mutator protein, dna replication
• Biological source: SULFOLOBUS SOLFATARICUS
• Cellular location: Cytoplasm (Probable): Q97W02
• Total number of polymer chains: 3
• Total formula weight: 51484.44

Authors

Irimia, A.,Egli, M. (deposition date: 2007-03-14, release date: 2007-05-08, Last modification date: 2023-12-13)

Primary citation

Eoff, R.L.,Irimia, A.,Angel, K.C.,Egli, M.,Guengerich, F.P.
Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4.
J.Biol.Chem., 282:19831-, 2007

PubMed Abstract: Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) has been shown to catalyze bypass of 7,8-dihydro-8-oxodeoxyguanosine (8-oxoG) in a highly efficient and relatively accurate manner. Crystal structures have revealed a potential role for Arg(332) in stabilizing the anti conformation of the 8-oxoG template base by means of a hydrogen bond or ion-dipole pair, which results in an increased enzymatic efficiency for dCTP insertion and makes formation of a Hoogsteen pair between 8-oxoG and dATP less favorable. Site-directed mutagenesis was used to replace Arg(332) with Ala, Glu, Leu, or His in order to probe the importance of Arg(332) in accurate and efficient bypass of 8-oxoG. The double mutant Ala(331)Ala(332) was also prepared to address the contribution of Arg(331). Transientstate kinetic results suggest that Glu(332) retains fidelity against bypass of 8-oxoG that is similar to wild type Dpo4, a result that was confirmed by tandem mass spectrometric analysis of full-length extension products. A crystal structure of the Dpo4 Glu(332) mutant and 8-oxoG:C pair revealed water-mediated hydrogen bonds between Glu(332) and the O-8 atom of 8-oxoG. The space normally occupied by Arg(332) side chain is empty in the crystal structures of the Ala(332) mutant. Two other crystal structures show that a Hoogsteen base pair is formed between 8-oxoG and A in the active site of both Glu(332) and Ala(332) mutants. These results support the view that a bond between Arg(332) and 8-oxoG plays a role in determining the fidelity and efficiency of Dpo4-catalyzed bypass of the lesion.

PubMed: 17468100
DOI: 10.1074/JBC.M702290200

Experimental method

X-RAY DIFFRACTION (2.09 Å)