6LAE

Crystal structure of the DNA-binding domain of human XPA in complex with DNA

6LAE の概要

• エントリーDOI: 10.2210/pdb6lae/pdb
• 分子名称: DNA repair protein complementing XP-A cells, DNA (5'-D(P*GP*CP*AP*TP*CP*TP*CP*GP*CP*CP*T)-3'), DNA (5'-D(P*TP*GP*GP*CP*GP*AP*GP*AP*TP*GP*C)-3'), ... (5 entities in total)
• 機能のキーワード: protein-dna complex, nucleotide excision repair, dna repair, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 41776.54

構造登録者

Lian, F.M.,Yang, X.,Jiang, Y.L.,Yang, F.,Li, C.,Yang, W.,Qian, C. (登録日: 2019-11-12, 公開日: 2020-02-26, 最終更新日: 2023-11-22)

主引用文献

Lian, F.M.,Yang, X.,Jiang, Y.L.,Yang, F.,Li, C.,Yang, W.,Qian, C.
New structural insights into the recognition of undamaged splayed-arm DNA with a single pair of non-complementary nucleotides by human nucleotide excision repair protein XPA.
Int.J.Biol.Macromol., 148:466-474, 2020

PubMed Abstract: XPA (Xeroderma pigmentosum complementation group A) is a core scaffold protein that plays significant roles in DNA damage verification and recruiting downstream endonucleases in the nucleotide excision repair (NER) pathway. Here, we present the 2.81 Å resolution crystal structure of the DNA-binding domain (DBD) of human XPA in complex with an undamaged splayed-arm DNA substrate with a single pair of non-complementary nucleotides. The structure reveals that two XPA molecules bind to one splayed-arm DNA with a 10-bp duplex recognition motif in a non-sequence-specific manner. XPA molecules bind to both ends of the DNA duplex region with a characteristic β-hairpin. A conserved tryptophan residue Trp175 packs against the last base pair of DNA duplex and stabilizes the conformation of the characteristic β-hairpin. Upon DNA binding, the C-terminal last helix of XPA would shift towards the minor groove of the DNA substrate for better interaction. Notably, human XPA is able to bind to the undamaged DNA duplex without any kinks, and XPA-DNA binding does not bend the DNA substrate obviously. This study provides structural basis for the binding mechanism of XPA to the undamaged splayed-arm DNA with a single pair of non-complementary nucleotides.

PubMed: 31962067
DOI: 10.1016/j.ijbiomac.2020.01.169

実験手法

X-RAY DIFFRACTION (2.81 Å)