2fdc: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:2fdc.png|left|200px]]
-<!--
+==Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex==
-The line below this paragraph, containing "STRUCTURE_2fdc", creates the "Structure Box" on the page.
+<StructureSection load='2fdc' size='340' side='right'caption='[[2fdc]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2fdc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FDC FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLQ:N-[6-(ACETYLAMINO)HEXYL]-3,6-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9-XANTHENE]-6-CARBOXAMIDE'>FLQ</scene></td></tr>
-{{STRUCTURE_2fdc|  PDB=2fdc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fdc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdc OCA], [https://pdbe.org/2fdc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fdc RCSB], [https://www.ebi.ac.uk/pdbsum/2fdc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UVRB_BACCA UVRB_BACCA] 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).[HAMAP-Rule:MF_00204]
+== 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/fd/2fdc_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/main_output.php?pdb_ID=2fdc ConSurf].
+<div style="clear:both"></div>
-===Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex===
+==See Also==
+*[[UvrABC|UvrABC]]
+__TOC__
-<!--
+</StructureSection>
-The line below this paragraph, {{ABSTRACT_PUBMED_16532007}}, adds the Publication Abstract to the page
+[[Category: Large Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16532007 is the PubMed ID number.
+[[Category: Kisker C]]
--->
+[[Category: Truglio JJ]]
-{{ABSTRACT_PUBMED_16532007}}
-==About this Structure==
-[[2fdc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldotenax Bacillus caldotenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDC OCA].
-==Reference==
-<ref group="xtra">PMID:016532007</ref><ref group="xtra">PMID:018578568</ref><references group="xtra"/>
-[[Category: Bacillus caldotenax]]
-[[Category: Kisker, C.]]
-[[Category: Truglio, J J.]]
-[[Category: Dna binding protein-dna complex]]
-[[Category: Dna repair]]
-[[Category: Ner]]
-[[Category: Nucleotide excision repair]]
-[[Category: Protein-dna complex]]
-[[Category: Uvra]]
-[[Category: Uvrb]]
-[[Category: Uvrc]]
-[[Category: Uvrd]]