EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA.
ジャーナル・号・ページ	Nat Commun, Vol. 17, Issue 1, Page 387, Year 2025
掲載日	2025年12月11日
著者	Shivlee Nirwal / Mariusz Czarnocki-Cieciura / Weronika Zajko / Krzysztof Skowronek / Roman H Szczepanowski / Marcin Nowotny /
PubMed 要旨	Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two ...Nucleotide excision repair is a DNA repair pathway which detects and fixes various DNA lesions that distort the structure of DNA. In bacteria, the pathway starts with the UvrA protein which has two adenosine triphosphatase modules and forms dimers. The DNA is handed over from UvrA to UvrB, which is a weak helicase that verifies the presence of damage. Despite intense studies, the role of the ATPase activity of UvrA in damage recognition is unclear. Here, we present a series of cryo-electron microscopy structures of UvrA in complex with three different DNAs and in the presence and absence of nucleotides. We also present a structure of UvrA:UvrB:DNA complex. These structures reveal a major rearrangement of the UvrA dimer upon ATP binding. We propose that these conformational changes are used to mechanically probe the integrity of DNA for damage localization. Collectively, our results present snapshots of UvrA's ATP-dependent DNA damage detection.
リンク	Nat Commun / PubMed:41381534 / PubMed Central
手法	EM (単粒子)
解像度	2.74 - 4.81 Å
構造データ	51665 9gxk EMDB-51665, PDB-9gxk: C. thermocellum UvrA (basal conformation) 手法: EM (単粒子) / 解像度: 2.97 Å 51666 9gxl EMDB-51666, PDB-9gxl: C. thermocellum UvrA in complex with AMPPNP (basal conformation) 手法: EM (単粒子) / 解像度: 2.96 Å 51667 9gxm EMDB-51667, PDB-9gxm: C. thermocellum UvrA in complex with unmodified DNA and AMPPNP (basal conformation) 手法: EM (単粒子) / 解像度: 3.23 Å 51668 9gxn EMDB-51668, PDB-9gxn: C. thermocellum UvrA in complex with unmodified DNA and AMPPNP (ATP-bound conformation 1) 手法: EM (単粒子) / 解像度: 3.14 Å 51669 9gxo EMDB-51669, PDB-9gxo: C. thermocellum UvrA in complex with unmodified DNA and AMPPNP (ATP-bound conformation 2) 手法: EM (単粒子) / 解像度: 3.1 Å 51670 9gxp EMDB-51670, PDB-9gxp: C. thermocellum UvrA in complex with DNA with an abasic site (basal conformation) 手法: EM (単粒子) / 解像度: 3.84 Å 51671 9gxq EMDB-51671, PDB-9gxq: C. thermocellum UvrA in complex with DNA with an abasic site and AMPPNP (ATP-bound conformation 1) 手法: EM (単粒子) / 解像度: 2.74 Å 51672 9gxr EMDB-51672, PDB-9gxr: C. thermocellum UvrA in complex with DNA with an abasic site and AMPPNP (ATP-bound conformation 2) 手法: EM (単粒子) / 解像度: 3.04 Å 51673 9gxs EMDB-51673, PDB-9gxs: C. thermocellum UvrA in complex with DNA with a fluorescein modification (basal conformation) 手法: EM (単粒子) / 解像度: 3.14 Å 51674 9gxt EMDB-51674, PDB-9gxt: C. thermocellum UvrA in complex with DNA with a fluorescein modification and AMPPNP (ATP-bound conformation 1) 手法: EM (単粒子) / 解像度: 3.1 Å 51675 9gxu EMDB-51675, PDB-9gxu: C. thermocellum UvrA (K647A) in complex with DNA with a fluorescein modification (basal conformation) 手法: EM (単粒子) / 解像度: 4.81 Å 51676 9gxv EMDB-51676, PDB-9gxv: C. thermocellum UvrA in complex with DNA with a fluorescein modification and ADP (basal conformation) 手法: EM (単粒子) / 解像度: 3.87 Å EMDB-51677: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP: consensus map 手法: EM (単粒子) / 解像度: 2.97 Å 51678 9gxw EMDB-51678, PDB-9gxw: C. thermocellum UvrA (K39A) in complex with DNA with a fluorescein modification and AMPPNP (basal conformation) 手法: EM (単粒子) / 解像度: 3.63 Å EMDB-51690: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP: focused map 手法: EM (単粒子) / 解像度: 3.18 Å 51691 9gy7 EMDB-51691: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP (composite map) PDB-9gy7: C. thermocellum UvrA-UvrB in complex with DNA with a fluorescein modification and AMPPNP 手法: EM (単粒子) / 解像度: 3.18 Å
化合物	ChemComp-ZN: Unknown entry ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP / AMP-PNP, エネルギー貯蔵分子類似体YM ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP / ADP, エネルギー貯蔵分子YM
由来	acetivibrio thermocellus (バクテリア) synthetic construct (人工物)
キーワード	DNA BINDING PROTEIN / DNA Repair pathway / Nucleotide excision repair pathway / NER