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==Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y29F bound to its catalytic divalent cation== | ==Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y29F bound to its catalytic divalent cation== | ||
<StructureSection load='1yd4' size='340' side='right' caption='[[1yd4]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='1yd4' size='340' side='right'caption='[[1yd4]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1yd4]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1yd4]] 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=1YD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD4 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd4 OCA], [https://pdbe.org/1yd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd4 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd4 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). | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd4_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd4_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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=1yd4 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 27: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 1yd4" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[UvrABC|UvrABC]] | *[[UvrABC 3D structures|UvrABC 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Thermotoga maritima]] | [[Category: Thermotoga maritima]] | ||
[[Category: Croteau | [[Category: Croteau DL]] | ||
[[Category: DellaVecchia | [[Category: DellaVecchia MJ]] | ||
[[Category: Karakas E]] | |||
[[Category: Karakas | [[Category: Kisker C]] | ||
[[Category: Kisker | [[Category: Rhau B]] | ||
[[Category: Rhau | [[Category: Skorvaga M]] | ||
[[Category: Skorvaga | [[Category: Truglio JJ]] | ||
[[Category: Truglio | [[Category: Van Houten B]] | ||
[[Category: | [[Category: Wang H]] | ||
[[Category: Wang | [[Category: Wang L]] | ||
[[Category: | |||
Latest revision as of 11:02, 15 May 2024
Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y29F bound to its catalytic divalent cationCrystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant Y29F bound to its catalytic divalent cation
Structural highlights
FunctionUVRC_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 Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedNucleotide 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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