3PR5

Dpo4 Y12A mutant incorporating ADP opposite template dT

Summary for 3PR5

• Entry DOI: 10.2210/pdb3pr5/pdb
• Descriptor: DNA polymerase IV, DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*C)-3'), DNA (5'-D(*TP*TP*CP*AP*TP*GP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'), ... (6 entities in total)
• Functional Keywords: dna polymerase, transferase-dna complex, transferase/dna
• Biological source: Sulfolobus solfataricus
• Cellular location: Cytoplasm (Probable): Q97W02
• Total number of polymer chains: 3
• Total formula weight: 48974.90

Authors

Kirouac, K.N.,Ling, H. (deposition date: 2010-11-29, release date: 2011-02-23, Last modification date: 2023-09-06)

Primary citation

Kirouac, K.N.,Suo, Z.,Ling, H.
Structural mechanism of ribonucleotide discrimination by a Y-family DNA polymerase.
J.Mol.Biol., 407:382-390, 2011

PubMed Abstract: The ability of DNA polymerases to differentiate between ribonucleotides and deoxribonucleotides is fundamental to the accurate replication and maintenance of an organism's genome. The active sites of Y-family DNA polymerases are highly solvent accessible, yet these enzymes still maintain a high selectivity towards deoxyribonucleotides. Here, we biochemically demonstrate that a single active-site mutation (Y12A) in Dpo4, a model Y-family DNA polymerase, causes both a dramatic loss of ribonucleotide discrimination and a decrease in nucleotide incorporation efficiency. We also determined two ternary crystal structures of the Dpo4 Y12A mutant incorporating either dATP or ATP nucleotides opposite a template dT base. Interestingly, both dATP and ATP were hydrolyzed to dADP and ADP, respectively. In addition, the dADP and ADP molecules adopt a similar conformation and position at the polymerase active site to a ddADP molecule in the ternary crystal structure of wild-type Dpo4. The Y12A mutant loses stacking interactions with the deoxyribose of dNTP, which destabilizes the binding of incoming nucleotides. The mutation also opens a space to accommodate the 2'-OH group of the ribose of NTP in the polymerase active site. The structural change leads to the reduction in deoxynucleotide incorporation efficiency and allows ribonucleotide incorporation.

PubMed: 21295588
DOI: 10.1016/j.jmb.2011.01.037

Experimental method

X-RAY DIFFRACTION (2.4 Å)