1d9x: Difference between revisions

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<StructureSection load='1d9x' size='340' side='right'caption='[[1d9x]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='1d9x' size='340' side='right'caption='[[1d9x]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1d9x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_caldotenax"_heinen_and_heinen_1972 "bacillus caldotenax" heinen and heinen 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D9X FirstGlance]. <br>
<table><tr><td colspan='2'>[[1d9x]] is a 1 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=1D9X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D9X FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1d9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d9x OCA], [https://pdbe.org/1d9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d9x RCSB], [https://www.ebi.ac.uk/pdbsum/1d9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d9x 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=1d9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d9x OCA], [https://pdbe.org/1d9x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d9x RCSB], [https://www.ebi.ac.uk/pdbsum/1d9x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d9x ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== 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]  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1d9x 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=1d9x ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism. NER systems recognize the damaged DNA strand, cleave it on both sides of the lesion, remove and newly synthesize the fragment. UvrB is a central component of the bacterial NER system participating in damage recognition, strand excision and repair synthesis. We have solved the crystal structure of UvrB in the apo and the ATP-bound forms. UvrB contains two domains related in structure to helicases, and two additional domains unique to repair proteins. The structure contains all elements of an intact helicase, and is evidence that UvrB utilizes ATP hydrolysis to move along the DNA to probe for damage. The location of conserved residues and structural comparisons allow us to predict the path of the DNA and suggest that the tight pre-incision complex of UvrB and the damaged DNA is formed by insertion of a flexible beta-hairpin between the two DNA strands.
Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair.,Theis K, Chen PJ, Skorvaga M, Van Houten B, Kisker C EMBO J. 1999 Dec 15;18(24):6899-907. PMID:10601012<ref>PMID:10601012</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1d9x" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[UvrABC|UvrABC]]
*[[UvrABC|UvrABC]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus caldotenax heinen and heinen 1972]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chen, P J]]
[[Category: Chen PJ]]
[[Category: Houten, B Van]]
[[Category: Kisker C]]
[[Category: Kisker, C]]
[[Category: Skorvaga M]]
[[Category: Skorvaga, M]]
[[Category: Theis K]]
[[Category: Theis, K]]
[[Category: Van Houten B]]
[[Category: Apo protein]]
[[Category: Gene regulation]]

Latest revision as of 09:51, 7 February 2024

CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRBCRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB

Structural highlights

1d9x is a 1 chain structure with sequence from Bacillus caldotenax. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1d9x, resolution 2.60Å

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