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| | <StructureSection load='4yir' size='340' side='right'caption='[[4yir]], [[Resolution|resolution]] 3.05Å' scene=''> | | <StructureSection load='4yir' size='340' side='right'caption='[[4yir]], [[Resolution|resolution]] 3.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4yir]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4u29 4u29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YIR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4yir]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4u29 4u29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YIR FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=G47:N2-ETHANETHIOL-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>G47</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]] 3.0501Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4u29|4u29]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G47:N2-ETHANETHIOL-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>G47</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RAD4, YER162C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RAD23, YEL037C, SYGP-ORF29 ([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=4yir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yir OCA], [https://pdbe.org/4yir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yir RCSB], [https://www.ebi.ac.uk/pdbsum/4yir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yir 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=4yir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yir OCA], [http://pdbe.org/4yir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yir RCSB], [http://www.ebi.ac.uk/pdbsum/4yir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yir ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RAD4_YEAST RAD4_YEAST]] Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. [[http://www.uniprot.org/uniprot/RAD23_YEAST RAD23_YEAST]] Plays a central role both in proteasomal degradation of misfolded proteins and DNA repair. Central component of a complex required to couple deglycosylation and proteasome-mediated degradation of misfolded proteins in the endoplasmic reticulum that are retrotranslocated in the cytosol. Involved in DNA excision repair. May play a part in DNA damage recognition and/or in altering chromatin structure to allow access by damage-processing enzymes. | + | [https://www.uniprot.org/uniprot/RAD4_YEAST RAD4_YEAST] Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. |
| | <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: Large Structures]] |
| - | [[Category: Chen, X]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Kim, Y]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Min, J H]] | + | [[Category: Chen X]] |
| - | [[Category: Beta-hairpin]] | + | [[Category: Kim Y]] |
| - | [[Category: Disulfide crosslinking]] | + | [[Category: Min J-H]] |
| - | [[Category: Dna binding protein-dna complex]]
| + | |
| - | [[Category: Dna damage repair]]
| + | |
| - | [[Category: Nucleotide excision repair]]
| + | |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Protein-dna crosslinking]]
| + | |
| - | [[Category: Protein-dna interaction]]
| + | |
| - | [[Category: Transglutaminase domain]]
| + | |
| - | [[Category: Xeroderma pigmentosum]]
| + | |
| Structural highlights
Function
RAD4_YEAST Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents.
Publication Abstract from PubMed
The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.
Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.,Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH Nat Commun. 2015 Jan 6;6:5849. doi: 10.1038/ncomms6849. PMID:25562780[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat Commun. 2015 Jan 6;6:5849. doi: 10.1038/ncomms6849. PMID:25562780 doi:http://dx.doi.org/10.1038/ncomms6849
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