+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDBB7 |
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Sample | Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA
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Function / homology | Function and homology information negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...negative regulation of nuclease activity / Defective Base Excision Repair Associated with NEIL1 / depyrimidination / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine 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 / 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, gap-filling / base-excision repair / chromosome / response to oxidative stress / damaged DNA binding / centrosome / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function |
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 ...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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDBB7 |
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-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-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) |
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-Sample
Sample | Name: Human NEI like DNA glycosylase 1 (NEIL1) bound to DNA / Specimen concentration: 1.30-2.10 / Entity id: 453 / 454 |
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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 ...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: dsDNADNA / 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 synchrotronSynchrotron / Wavelength: 1.127 Å / Dist. spec. to detc.: 1.4 mm | ||||||||||||||||||||||||||||||||||||||||||
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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 /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 910 /
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Result | Type of curve: single_conc Comments: The theoretical MW for this NEIL1/DNA complex is 55.8kDa.
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