1yd0: Difference between revisions

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<StructureSection load='1yd0' size='340' side='right'caption='[[1yd0]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='1yd0' size='340' side='right'caption='[[1yd0]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1yd0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1yd0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD0 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.5&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ln0|1ln0]], [[1mk0|1mk0]], [[1kft|1kft]], [[1d9x|1d9x]], [[1ycz|1ycz]], [[1yd1|1yd1]], [[1yd2|1yd2]], [[1yd3|1yd3]], [[1yd4|1yd4]], [[1yd5|1yd5]], [[1yd6|1yd6]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1yd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd0 OCA], [https://pdbe.org/1yd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd0 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd0 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=1yd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd0 OCA], [https://pdbe.org/1yd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd0 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/UVRC_THEMA UVRC_THEMA]] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision (By similarity).  
[https://www.uniprot.org/uniprot/UVRC_THEMA UVRC_THEMA] The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision (By similarity).
== 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=1yd0 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=1yd0 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nucleotide excision repair is a highly conserved DNA repair mechanism present in all kingdoms of life. The incision reaction is a critical step for damage removal and is accomplished by the UvrC protein in eubacteria. No structural information is so far available for the 3' incision reaction. Here we report the crystal structure of the N-terminal catalytic domain of UvrC at 1.5 A resolution, which catalyzes the 3' incision reaction and shares homology with the catalytic domain of the GIY-YIG family of intron-encoded homing endonucleases. The structure reveals a patch of highly conserved residues surrounding a catalytic magnesium-water cluster, suggesting that the metal binding site is an essential feature of UvrC and all GIY-YIG endonuclease domains. Structural and biochemical data strongly suggest that the N-terminal endonuclease domain of UvrC utilizes a novel one-metal mechanism to cleave the phosphodiester bond.
Structural insights into the first incision reaction during nucleotide excision repair.,Truglio JJ, Rhau B, Croteau DL, Wang L, Skorvaga M, Karakas E, DellaVecchia MJ, Wang H, Van Houten B, Kisker C EMBO J. 2005 Mar 9;24(5):885-94. Epub 2005 Feb 3. PMID:15692561<ref>PMID:15692561</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1yd0" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[UvrABC|UvrABC]]
*[[UvrABC|UvrABC]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 43589]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Croteau, D L]]
[[Category: Thermotoga maritima]]
[[Category: DellaVecchia, M J]]
[[Category: Croteau DL]]
[[Category: Houten, B Van]]
[[Category: DellaVecchia MJ]]
[[Category: Karakas, E]]
[[Category: Karakas E]]
[[Category: Kisker, C]]
[[Category: Kisker C]]
[[Category: Rhau, B]]
[[Category: Rhau B]]
[[Category: Skorvaga, M]]
[[Category: Skorvaga M]]
[[Category: Truglio, J J]]
[[Category: Truglio JJ]]
[[Category: Wang, H]]
[[Category: Van Houten B]]
[[Category: Wang, L]]
[[Category: Wang H]]
[[Category: Dna binding protein]]
[[Category: Wang L]]

Latest revision as of 13:37, 13 March 2024

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima bound to its catalytic divalent cation: manganese

1yd0, resolution 1.50Å

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