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| | ==The catalytic core of Rad2 in complex with DNA substrate (complex III)== | | ==The catalytic core of Rad2 in complex with DNA substrate (complex III)== |
| - | <StructureSection load='4q0z' size='340' side='right' caption='[[4q0z]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='4q0z' size='340' side='right'caption='[[4q0z]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4q0z]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q0Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4q0z]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q0Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.398Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4q0r|4q0r]], [[4q0w|4q0w]], [[4q10|4q10]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RAD2, YGR258C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4q0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0z OCA], [https://pdbe.org/4q0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q0z RCSB], [https://www.ebi.ac.uk/pdbsum/4q0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0z ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4q0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q0z OCA], [http://pdbe.org/4q0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q0z RCSB], [http://www.ebi.ac.uk/pdbsum/4q0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q0z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RAD2_YEAST RAD2_YEAST]] Single-stranded DNA endonuclease involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Essential for the incision step of excision-repair.<ref>PMID:8247134</ref> | + | [https://www.uniprot.org/uniprot/RAD2_YEAST RAD2_YEAST] Single-stranded DNA endonuclease involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Essential for the incision step of excision-repair.<ref>PMID:8247134</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | + | [[Category: Large Structures]] |
| - | [[Category: Jaciuk, M]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Kustosz, P]] | + | [[Category: Jaciuk M]] |
| - | [[Category: Mietus, M]] | + | [[Category: Kustosz P]] |
| - | [[Category: Nowak, E]] | + | [[Category: Mietus M]] |
| - | [[Category: Nowotny, M]] | + | [[Category: Nowak E]] |
| - | [[Category: Ba rossmann-like]]
| + | [[Category: Nowotny M]] |
| - | [[Category: Dna repair]]
| + | |
| - | [[Category: Hydrolase-dna complex]]
| + | |
| - | [[Category: Tfiih]]
| + | |
| Structural highlights
Function
RAD2_YEAST Single-stranded DNA endonuclease involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Essential for the incision step of excision-repair.[1]
Publication Abstract from PubMed
Rad2/XPG belongs to the flap nuclease family and is responsible for a key step of the eukaryotic nucleotide excision DNA repair (NER) pathway. To elucidate the mechanism of DNA binding by Rad2/XPG, we solved crystal structures of the catalytic core of Rad2 in complex with a substrate. Rad2 utilizes three structural modules for recognition of the double-stranded portion of DNA substrate, particularly a Rad2-specific alpha-helix for binding the cleaved strand. The protein does not specifically recognize the single-stranded portion of the nucleic acid. Our data suggest that in contrast to related enzymes (FEN1 and EXO1), the Rad2 active site may be more accessible, which would create an exit route for substrates without a free 5' end.
Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding.,Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M Nucleic Acids Res. 2014 Aug 12. pii: gku729. PMID:25120270[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Habraken Y, Sung P, Prakash L, Prakash S. Yeast excision repair gene RAD2 encodes a single-stranded DNA endonuclease. Nature. 1993 Nov 25;366(6453):365-8. PMID:8247134 doi:http://dx.doi.org/10.1038/366365a0
- ↑ Mietus M, Nowak E, Jaciuk M, Kustosz P, Studnicka J, Nowotny M. Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Nucleic Acids Res. 2014 Aug 12. pii: gku729. PMID:25120270 doi:http://dx.doi.org/10.1093/nar/gku729
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