3v4r: Difference between revisions

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<StructureSection load='3v4r' size='340' side='right'caption='[[3v4r]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
<StructureSection load='3v4r' size='340' side='right'caption='[[3v4r]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3v4r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V4R FirstGlance]. <br>
<table><tr><td colspan='2'>[[3v4r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V4R FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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]] 3.25&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU35170, dinA, uvr, uvrB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Type_III_site-specific_deoxyribonuclease Type III site-specific deoxyribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.5 3.1.21.5] </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=3v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v4r OCA], [https://pdbe.org/3v4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v4r RCSB], [https://www.ebi.ac.uk/pdbsum/3v4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v4r ProSAT]</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=3v4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v4r OCA], [https://pdbe.org/3v4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v4r RCSB], [https://www.ebi.ac.uk/pdbsum/3v4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v4r ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/UVRB_BACSU UVRB_BACSU]] 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_BACSU UVRB_BACSU] 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).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
UvrB has a central role in the highly conserved UvrABC pathway functioning not only as a damage recognition element but also as an essential component of the lesion tracking machinery. While it has been recently confirmed that the tracking assembly comprises a UvrA(2)B(2) heterotetramer, the configurations of the damage engagement and UvrB-DNA handover complexes remain obscure. Here, we present the first crystal structure of a UvrB dimer whose biological significance has been verified using both chemical cross-linking and electron paramagnetic resonance spectroscopy. We demonstrate that this dimeric species stably associates with UvrA and forms a UvrA(2)B(2)-DNA complex. Our studies also illustrate how signals are transduced between the ATP and DNA binding sites to generate the helicase activity pivotal to handover and formation of the UvrB(2)-DNA complex, providing key insights into the configurations of these important repair intermediates.
 
Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB-DNA complexes.,Webster MP, Jukes R, Zamfir VS, Kay CW, Bagneris C, Barrett T Nucleic Acids Res. 2012 Sep 1;40(17):8743-8758. Epub 2012 Jun 30. PMID:22753105<ref>PMID:22753105</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3v4r" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[UvrABC|UvrABC]]
*[[UvrABC|UvrABC]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Type III site-specific deoxyribonuclease]]
[[Category: Barrett T]]
[[Category: Barrett, T]]
[[Category: Jukes R]]
[[Category: Jukes, R]]
[[Category: Webster MPJ]]
[[Category: Webster, M P.J]]
[[Category: Atp hydrolysis]]
[[Category: Dna helicase]]
[[Category: Helicase motifs and a beta-hairpin]]
[[Category: Hydrolase-dna complex]]
[[Category: Uvra]]

Latest revision as of 17:17, 14 March 2024

Crystal structure of a UvrB dimer-DNA complexCrystal structure of a UvrB dimer-DNA complex

Structural highlights

3v4r is a 4 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.25Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UVRB_BACSU 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).

See Also

3v4r, resolution 3.25Å

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