3BQ1

Insertion ternary complex of Dbh DNA polymerase

3BQ1 の概要

• エントリーDOI: 10.2210/pdb3bq1/pdb
• 関連するPDBエントリー: 3BQ0 3BQ2
• 分子名称: DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3'), DNA (5'-D(*DT*DTP*DCP*DCP*DGP*DCP*DCP*DCP*DGP*DGP*DCP*DTP*DTP*DCP*DC)-3'), DNA polymerase IV, ... (6 entities in total)
• 機能のキーワード: dna polymerase, y-family, lesion bypass, single-base deletion, -1 frameshift, dna damage, dna repair, dna replication, dna-binding, dna-directed dna polymerase, magnesium, metal-binding, mutator protein, nucleotidyltransferase, transferase, transferase-dna complex, transferase/dna
• 由来する生物種: Sulfolobus acidocaldarius
• 細胞内の位置: Cytoplasm (Probable): Q4JB80
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 48145.01

構造登録者

Pata, J.D.,Wilson, R.C. (登録日: 2007-12-19, 公開日: 2008-04-08, 最終更新日: 2023-08-30)

主引用文献

Wilson, R.C.,Pata, J.D.
Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh.
Mol.Cell, 29:767-779, 2008

PubMed Abstract: Dbh is a Y family translesion DNA polymerase that accurately bypasses some damaged forms of deoxyguanosine, but also generates single-base deletion errors at frequencies of up to 50%, in specific hot spot sequences. We describe preinsertion binary, insertion ternary, and postinsertion binary crystal structures of Dbh synthesizing DNA after making a single-base deletion. The skipped template base adopts an extrahelical conformation stabilized by interactions with the C-terminal domain of the enzyme. DNA translocation and positioning of the next templating base at the active site, with space opposite to accommodate incoming nucleotide, occur independently of nucleotide binding, incorporation, and pyrophosphate release. We also show that Dbh creates single-base deletions more rapidly when the skipped base is located two or three bases upstream of the nascent base pair than when it is directly adjacent to the templating base, indicating that Dbh predominantly creates single-base deletions by template slippage rather than by dNTP-stabilized misalignment.

PubMed: 18374650
DOI: 10.1016/j.molcel.2008.01.014

実験手法

X-RAY DIFFRACTION (2.7 Å)