1d2m: Difference between revisions

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-{{Seed}}
-[[Image:1d2m.png|left|200px]]
-<!--
+==UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME==
-The line below this paragraph, containing "STRUCTURE_1d2m", creates the "Structure Box" on the page.
+<StructureSection load='1d2m' size='340' side='right'caption='[[1d2m]], [[Resolution|resolution]] 1.90&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'>[[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>
-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]] 1.9&#8491;</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>
-{{STRUCTURE_1d2m|  PDB=1d2m  |  SCENE=  }}
+<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 ==
+[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>
+    <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=1d2m ConSurf].
+<div style="clear:both"></div>
-===UVRB PROTEIN OF THERMUS THERMOPHILUS HB8; A NUCLEOTIDE EXCISION REPAIR ENZYME===
+==See Also==
+*[[UvrABC|UvrABC]]
+__TOC__
-<!--
+</StructureSection>
-The line below this paragraph, {{ABSTRACT_PUBMED_10578047}}, adds the Publication Abstract to the page
+[[Category: Large Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10578047 is the PubMed ID number.
+[[Category: Thermus thermophilus HB8]]
--->
+[[Category: Fukuyama K]]
-{{ABSTRACT_PUBMED_10578047}}
+[[Category: Kato R]]
+[[Category: Kuramitsu S]]
-==About this Structure==
+[[Category: Masui R]]
-D2M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D2M OCA].
+[[Category: Nakagawa N]]
+[[Category: Sugahara M]]
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/10578047 10578047]
-[[Category: Single protein]]
-[[Category: Thermus thermophilus]]
-[[Category: Fukuyama, K.]]
-[[Category: Kato, R.]]
-[[Category: Kuramitsu, S.]]
-[[Category: Masui, R.]]
-[[Category: Nakagawa, N.]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
-[[Category: Sugahara, M.]]
-[[Category: Multidomain protein]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:12:32 2008''