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

Basic information

• Entry: Database: SASBDB / ID: SASDBB7

Sample

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

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

Function / homology

Function:

: / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol

Domain/homology:

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

Component:

Endonuclease 8-like 1

• Biological species: Homo sapiens (human)
• Citation: Journal: Nucleic Acids Res / Year: 2017; Title: Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase.; Authors: Aishwarya Prakash / Kedar Moharana / Susan S Wallace / Sylvie Doublié / ; Abstract: 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.

Contact author

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

Models

• Model #810: ; Type: dummy / Software: DAMMIN / Radius of dummy atoms: 4.50 A / Chi-square value: 0.542; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA / Specimen concentration: 1.30-2.10 / Entity id: 453 / 454
• Buffer: Name: 25mM HEPES 100mM NaCl 1mM DTT / pH: 7.5

Entity #453

Type: protein / Description: Endonuclease 8-like 1 / Formula weight: 44.722 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q96FI4
Sequence:

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

Entity #454

Type: DNA / Description: dsDNA / Formula weight: 2.424 / Num. of mol.: 1
Sequence:

GCGTCCAGTC TACCCGCAGG TCCAGATGG

Experimental information

• Beam: Instrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS); City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotron / Wavelength: 1.127 Å / Dist. spec. to detc.: 1.4 mm
• Detector: Name: Pilatus3 X 2M / Pixsize x: 172 mm

Scan

Title: Human NEI like DNA glycosylase 1 (NEIL1) bound to / Measurement date: Jan 20, 2016 / Storage temperature: 4 °C / Cell temperature: 10 °C / Exposure time: 0.2 sec. / Number of frames: 24 / Unit: 1/A /

	Min	Max
Q	0.0164	0.5285

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 910 /

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

Result

Type of curve: single_conc
Comments: The theoretical MW for this NEIL1/DNA complex is 55.8kDa.

	Experimental	Standard	Standard error	Porod
MW	61.5 kDa	56.9 kDa	0.385	54.142 kDa
Volume	-	-	-	92.04 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	337	6.402	309	2.09
Radius of gyration, Rg	4.1 nm	0.123	3.3 nm	0.178

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