1d2m: Difference between revisions

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 ==UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME==
-<StructureSection load='1d2m' size='340' side='right' caption='[[1d2m]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1d2m' size='340' side='right'caption='[[1d2m]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1d2m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D2M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1D2M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1d2m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D2M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9&#8491;</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=1d2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d2m OCA], [http://pdbe.org/1d2m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1d2m RCSB], [http://www.ebi.ac.uk/pdbsum/1d2m PDBsum], [http://www.topsan.org/Proteins/RSGI/1d2m TOPSAN]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1d2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d2m OCA], [https://pdbe.org/1d2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d2m RCSB], [https://www.ebi.ac.uk/pdbsum/1d2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d2m ProSAT], [https://www.topsan.org/Proteins/RSGI/1d2m TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UVRB_THET8 UVRB_THET8]] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).
+[https://www.uniprot.org/uniprot/UVRB_THET8 UVRB_THET8] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. A damage recognition complex composed of 2 UvrA and 2 UvrB subunits scans DNA for abnormalities. Upon binding of the UvrA(2)B(2) complex to a putative damaged site, the DNA wraps around one UvrB monomer. DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix, facilitating insertion of UvrB beta-hairpin between the DNA strands. Then UvrB probes one DNA strand for the presence of a lesion. If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. This complex is subsequently bound by UvrC and the second UvrB is released. If no lesion is found, the DNA wraps around the other UvrB subunit that will check the other stand for damage (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/1d2m_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d2/1d2m_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1d2m ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-In the nucleotide excision repair system, UvrB plays a central role in damage recognition and DNA incision by interacting with UvrA and UvrC. We have determined the crystal structure of Thermus thermophilus HB8 UvrB at 1.9 A resolution. UvrB comprises four domains, two of which have an alpha/beta structure resembling the core domains of DNA and RNA helicases. Additionally, UvrB has an alpha-helical domain and a domain consisting of antiparallel beta-sheets (beta-domain). The sequence similarity suggests that the beta-domain interacts with UvrA. Based on the distribution of the conserved regions and the structure of the PcrA-DNA complex, a model for the UvrB-DNA complex is proposed.
-Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair.,Nakagawa N, Sugahara M, Masui R, Kato R, Fukuyama K, Kuramitsu S J Biochem. 1999 Dec;126(6):986-90. PMID:10578047<ref>PMID:10578047</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1d2m" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[UvrABC|UvrABC]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Thet8]]
+[[Category: Large Structures]]
-[[Category: Fukuyama, K]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Kato, R]]
+[[Category: Fukuyama K]]
-[[Category: Kuramitsu, S]]
+[[Category: Kato R]]
-[[Category: Masui, R]]
+[[Category: Kuramitsu S]]
-[[Category: Nakagawa, N]]
+[[Category: Masui R]]
-[[Category: Structural genomic]]
+[[Category: Nakagawa N]]
-[[Category: Sugahara, M]]
+[[Category: Sugahara M]]
-[[Category: Hydrolase]]
-[[Category: Multidomain protein]]
-[[Category: Rsgi]]