SASDBB7: Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA

基本情報

• 登録情報: データベース: SASBDB / ID: SASDBB7

試料

Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA

• Endonuclease 8-like 1 (protein), Homo sapiens
• dsDNA (DNA)

機能・相同性

分子機能:

negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / 加水分解酵素; 糖加水分解酵素; N-グリコシル化合物加水分解酵素 / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm

ドメイン・相同性:

Endonuclease VIII-like 1, DNA binding / Endonuclease VIII-like 1, DNA bind / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Ribosomal protein S13-like, H2TH

構成要素:

Endonuclease 8-like 1

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: Nucleic Acids Res / 年: 2017; タイトル: Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.; 著者: Aishwarya Prakash / Kedar Moharana / Susan S Wallace / Sylvie Doublié / ; 要旨: The base excision repair (BER) pathway repairs oxidized lesions in the DNA that result from reactive oxygen species generated in cells. If left unrepaired, these damaged DNA bases can disrupt cellular processes such as replication. NEIL1 is one of the 11 human DNA glycosylases that catalyze the first step of the BER pathway, i.e. recognition and excision of DNA lesions. NEIL1 interacts with essential replication proteins such as the ring-shaped homotrimeric proliferating cellular nuclear antigen (PCNA). We isolated a complex formed between NEIL1 and PCNA (±DNA) using size exclusion chromatography (SEC). This interaction was confirmed using native gel electrophoresis and mass spectrometry. Stokes radii measured by SEC hinted that PCNA in complex with NEIL1 (±DNA) was no longer a trimer. Height measurements and images obtained by atomic force microscopy also demonstrated the dissociation of the PCNA homotrimer in the presence of NEIL1 and DNA, while small-angle X-ray scattering analysis confirmed the NEIL1 mediated PCNA trimer dissociation and formation of a 1:1:1 NEIL1-DNA-PCNA(monomer) complex. Furthermore, ab initio shape reconstruction provides insights into the solution structure of this previously unreported complex. Together, these data point to a potential mechanistic switch between replication and BER.

登録者

• Kedar Moharana (University of Vermont, Burlington, VT, USA)

モデル

• モデル #810: ; タイプ: dummy / ソフトウェア: DAMMIN / ダミー原子の半径: 4.50 A / カイ2乗値: 0.542; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA; 試料濃度: 1.30-2.10 / Entity id: 453 / 454
• バッファ: 名称: 25mM HEPES 100mM NaCl 1mM DTT / pH: 7.5

要素 #453

タイプ: protein / 記述: Endonuclease 8-like 1 / 分子量: 44.722 / 分子数: 1 / 由来: Homo sapiens / 参照: UniProt: Q96FI4
配列:

MPEGPELHLA SQFVNEACRA LVFGGCVEKS SVSRNPEVPF ESSAYRISAS ARGKELRLIL SPLPGAQPQQ EPLALVFRFG MSGSFQLVPR EELPRHAHLR FYTAPPGPRL ALCFVDIRRF GRWDLGGKWQ PGRGPCVLQE YQQFRESVLR NLADKAFDRP ICEALLDQRF FNGIGNYLRA EILYRLKIPP FEKARSVLEA LQQHRPSPEL TLSQKIRTKL QNPDLLELCH SVPKEVVQLG GKGYGSESGE EDFAAFRAWL RCYGMPGMSS LQDRHGRTIW FQGDPGPLAP KGRKSRKKKS KATQLSPEDR VEDALPPSKA PSRTRRAKRD LPKRTATQRP EGTSLQQDPE APTVPKKGRR KGRQAASGHC RPRKVKADIP SLEPEGTSAS LEHHHHHH

要素 #454

タイプ: DNA / 記述: dsDNA / 分子量: 2.424 / 分子数: 1
配列:

GCGTCCAGTC TACCCGCAGG TCCAGATGG

実験情報

• ビーム: 設備名称: Advanced Light Source (ALS) 12.3.1 (SIBYLS) / 地域: Berkeley, CA / 国: USA / 線源: X-ray synchrotron / 波長: 1.127 Å / スペクトロメータ・検出器間距離: 1.4 mm
• 検出器: 名称: Pilatus3 X 2M / Pixsize x: 172 mm

スキャン

タイトル: Human NEI like DNA glycosylase 1 (NEIL1) bound to
測定日: 2016年1月20日 / 保管温度: 4 °C / セル温度: 10 °C / 照射時間: 0.2 sec. / フレーム数: 24 / 単位: 1/A /

	Min	Max
Q	0.0164	0.5285

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 910 /

	Min	Max
Q	0.022019	0.528544
P(R) point	1	910
R	0	175

結果

カーブのタイプ: single_conc
コメント: The theoretical MW for this NEIL1/DNA complex is 55.8kDa.

	実験値	Standard	Standard error	Porod
分子量	61.5 kDa	56.9 kDa	0.385	54.142 kDa
体積	-	-	-	92.04 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	337	6.402	309	2.09
慣性半径, Rg	4.1 nm	0.123	3.3 nm	0.178

	Min	Max	Error
D	-	17.5	1.6
Guinier point	11	42	-