3L8B

Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin

Summary for 3L8B

• Entry DOI: 10.2210/pdb3l8b/pdb
• Related: 1IG9 1Q9Y 2DY4 2P5O
• Descriptor: DNA polymerase, DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3'), ... (5 entities in total)
• Functional Keywords: dna polymerase rb69 gp43, protein-dna complex, oxidative dna lesion, guanidinohydantoin, dna replication, dna-binding, dna-directed dna polymerase, exonuclease, hydrolase, nuclease, nucleotidyltransferase, transferase, transferase-dna complex, transferase/dna
• Biological source: Enterobacteria phage RB69 (Bacteriophage RB69)
• Total number of polymer chains: 6
• Total formula weight: 229359.68

Authors

Aller, P.,Ye, Y.,Wallace, S.S.,Burrows, C.J.,Doublie, S. (deposition date: 2009-12-30, release date: 2010-03-09, Last modification date: 2023-09-06)

Primary citation

Aller, P.,Ye, Y.,Wallace, S.S.,Burrows, C.J.,Doublie, S.
Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin.
Biochemistry, 49:2502-2509, 2010

PubMed Abstract: The oxidation of guanine generates one of the most common DNA lesions, 8-oxo-7,8-dihydroguanine (8-oxoG). The further oxidation of 8-oxoG can produce either guanidinohydantoin (Gh) in duplex DNA or spiroiminodihydantoin (Sp) in nucleosides and ssDNA. Although Gh can be a strong block for replicative DNA polymerases such as RB69 DNA polymerase, this lesion is also mutagenic: DNA polymerases bypass Gh by preferentially incorporating a purine with a slight preference for adenine, which results in G.C --> T.A or G.C --> C.G transversions. The 2.15 A crystal structure of the replicative RB69 DNA polymerase in complex with DNA containing Gh reveals that Gh is extrahelical and rotated toward the major groove. In this conformation Gh is no longer in position to serve as a templating base for the incorporation of an incoming nucleotide. This work also constitutes the first crystallographic structure of Gh, which is stabilized in the R configuration in the two polymerase/DNA complexes present in the crystal asymmetric unit. In contrast to 8-oxoG, Gh is found in a high syn conformation in the DNA duplex and therefore presents the same hydrogen bond donor and acceptor pattern as thymine, which explains the propensity of DNA polymerases to incorporate a purine opposite Gh when bypass occurs.

PubMed: 20166752
DOI: 10.1021/bi902195p

Experimental method

X-RAY DIFFRACTION (2.15 Å)