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| | <StructureSection load='2vsf' size='340' side='right'caption='[[2vsf]], [[Resolution|resolution]] 2.90Å' scene=''> | | <StructureSection load='2vsf' size='340' side='right'caption='[[2vsf]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2vsf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VSF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VSF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2vsf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VSF FirstGlance]. <br> |
| - | </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=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.9Å</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2vsf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vsf OCA], [http://pdbe.org/2vsf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vsf RCSB], [http://www.ebi.ac.uk/pdbsum/2vsf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vsf ProSAT]</span></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=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=2vsf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vsf OCA], [https://pdbe.org/2vsf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vsf RCSB], [https://www.ebi.ac.uk/pdbsum/2vsf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vsf ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/XPD_THEAC XPD_THEAC]] ATP-dependent 5'-3' DNA helicase involved in nucleotide excision repair (NER) of DNA (By similarity). | + | [https://www.uniprot.org/uniprot/XPD_THEAC XPD_THEAC] ATP-dependent 5'-3' DNA helicase involved in nucleotide excision repair (NER) of DNA (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kisker, C]] | + | [[Category: Thermoplasma acidophilum]] |
| - | [[Category: Kuper, J]] | + | [[Category: Kisker C]] |
| - | [[Category: Truglio, J J]] | + | [[Category: Kuper J]] |
| - | [[Category: Wolski, S C]] | + | [[Category: Truglio JJ]] |
| - | [[Category: Atp-binding]] | + | [[Category: Wolski SC]] |
| - | [[Category: Helicase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Iron sulfur cluster]]
| + | |
| - | [[Category: Ner]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Tfiih]]
| + | |
| Structural highlights
Function
XPD_THEAC ATP-dependent 5'-3' DNA helicase involved in nucleotide excision repair (NER) of DNA (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
DNA damage recognition by the nucleotide excision repair pathway requires an initial step identifying helical distortions in the DNA and a proofreading step verifying the presence of a lesion. This proofreading step is accomplished in eukaryotes by the TFIIH complex. The critical damage recognition component of TFIIH is the XPD protein, a DNA helicase that unwinds DNA and identifies the damage. Here, we describe the crystal structure of an archaeal XPD protein with high sequence identity to the human XPD protein that reveals how the structural helicase framework is combined with additional elements for strand separation and DNA scanning. Two RecA-like helicase domains are complemented by a 4Fe4S cluster domain, which has been implicated in damage recognition, and an alpha-helical domain. The first helicase domain together with the helical and 4Fe4S-cluster-containing domains form a central hole with a diameter sufficient in size to allow passage of a single stranded DNA. Based on our results, we suggest a model of how DNA is bound to the XPD protein, and can rationalize several of the mutations in the human XPD gene that lead to one of three severe diseases, xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy.
Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD.,Wolski SC, Kuper J, Hanzelmann P, Truglio JJ, Croteau DL, Van Houten B, Kisker C PLoS Biol. 2008 Jun 24;6(6):e149. PMID:18578568[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wolski SC, Kuper J, Hanzelmann P, Truglio JJ, Croteau DL, Van Houten B, Kisker C. Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD. PLoS Biol. 2008 Jun 24;6(6):e149. PMID:18578568 doi:10.1371/journal.pbio.0060149
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