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| | ==XPD mechanism== | | ==XPD mechanism== |
| - | <StructureSection load='5h8w' size='340' side='right' caption='[[5h8w]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='5h8w' size='340' side='right'caption='[[5h8w]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5h8w]] is a 2 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=5H8W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H8W FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5h8w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H8W FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Ta0057 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </span></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=5h8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8w OCA], [https://pdbe.org/5h8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h8w RCSB], [https://www.ebi.ac.uk/pdbsum/5h8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8w 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=5h8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8w OCA], [http://pdbe.org/5h8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8w RCSB], [http://www.ebi.ac.uk/pdbsum/5h8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8w 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). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5h8w" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5h8w" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Helicase 3D structures|Helicase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: DNA helicase]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Constantinescu, D]] | + | [[Category: Large Structures]] |
| - | [[Category: Naismith, J H]] | + | [[Category: Thermoplasma acidophilum]] |
| - | [[Category: Helicase]] | + | [[Category: Constantinescu D]] |
| - | [[Category: Hydrolase]] | + | [[Category: Naismith JH]] |
| Structural highlights
Function
XPD_THEAC ATP-dependent 5'-3' DNA helicase involved in nucleotide excision repair (NER) of DNA (By similarity).
Publication Abstract from PubMed
The xeroderma pigmentosum group D (XPD) helicase is a component of the transcription factor IIH complex in eukaryotes and plays an essential role in DNA repair in the nucleotide excision repair pathway. XPD is a 5' to 3' helicase with an essential iron-sulfur cluster. Structural and biochemical studies of the monomeric archaeal XPD homologues have aided a mechanistic understanding of this important class of helicase, but several important questions remain open. In particular, the mechanism for DNA loading, which is assumed to require large protein conformational change, is not fully understood. Here, DNA binding by the archaeal XPD helicase from Thermoplasma acidophilum has been investigated using a combination of crystallography, cross-linking, modified substrates and biochemical assays. The data are consistent with an initial tight binding of ssDNA to helicase domain 2, followed by transient opening of the interface between the Arch and 4FeS domains, allowing access to a second binding site on helicase domain 1 that directs DNA through the pore. A crystal structure of XPD from Sulfolobus acidocaldiarius that lacks helicase domain 2 has an otherwise unperturbed structure, emphasizing the stability of the interface between the Arch and 4FeS domains in XPD.
Mechanism of DNA loading by the DNA repair helicase XPD.,Constantinescu-Aruxandei D, Petrovic-Stojanovska B, Penedo JC, White MF, Naismith JH Nucleic Acids Res. 2016 Feb 20. pii: gkw102. PMID:26896802[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Constantinescu-Aruxandei D, Petrovic-Stojanovska B, Penedo JC, White MF, Naismith JH. Mechanism of DNA loading by the DNA repair helicase XPD. Nucleic Acids Res. 2016 Feb 20. pii: gkw102. PMID:26896802 doi:http://dx.doi.org/10.1093/nar/gkw102
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