1yd5

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(New page: 200px<br /><applet load="1yd5" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yd5, resolution 1.80&Aring;" /> '''Crystal structure of...)
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[[Image:1yd5.gif|left|200px]]<br /><applet load="1yd5" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1yd5, resolution 1.80&Aring;" />
 
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'''Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant N88A bound to its catalytic divalent cation'''<br />
 
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==Overview==
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==Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant N88A bound to its catalytic divalent cation==
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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.
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<StructureSection load='1yd5' size='340' side='right'caption='[[1yd5]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1yd5]] 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=1YD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YD5 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yd5 OCA], [https://pdbe.org/1yd5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yd5 RCSB], [https://www.ebi.ac.uk/pdbsum/1yd5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yd5 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yd/1yd5_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1yd5 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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1YD5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YD5 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15692561 15692561]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1yd5" style="background-color:#fffaf0;"></div>
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[[Category: Thermotoga maritima]]
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[[Category: Croteau, D.L.]]
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[[Category: DellaVecchia, M.J.]]
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[[Category: Houten, B.Van.]]
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[[Category: Karakas, E.]]
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[[Category: Kisker, C.]]
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[[Category: Rhau, B.]]
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[[Category: Skorvaga, M.]]
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[[Category: Truglio, J.J.]]
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[[Category: Wang, H.]]
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[[Category: Wang, L.]]
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[[Category: MN]]
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[[Category: dna binding protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 06:41:43 2007''
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==See Also==
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*[[UvrABC 3D structures|UvrABC 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Thermotoga maritima]]
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[[Category: Croteau DL]]
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[[Category: DellaVecchia MJ]]
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[[Category: Karakas E]]
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[[Category: Kisker C]]
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[[Category: Rhau B]]
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[[Category: Skorvaga M]]
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[[Category: Truglio JJ]]
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[[Category: Van Houten B]]
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[[Category: Wang H]]
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[[Category: Wang L]]

Current revision

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima: Point mutant N88A bound to its catalytic divalent cation

PDB ID 1yd5

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