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3nkd

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[[Image:3nkd.png|left|200px]]
 
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==Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12==
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The line below this paragraph, containing "STRUCTURE_3nkd", creates the "Structure Box" on the page.
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<StructureSection load='3nkd' size='340' side='right' caption='[[3nkd]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3nkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecod1 Ecod1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NKD FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nke|3nke]], [[3god|3god]]</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EcDH1_0933 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=536056 ECOD1])</td></tr>
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{{STRUCTURE_3nkd| PDB=3nkd | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3nkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nkd OCA], [http://pdbe.org/3nkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nkd RCSB], [http://www.ebi.ac.uk/pdbsum/3nkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nkd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[http://www.uniprot.org/uniprot/C9R0C6_ECOD1 C9R0C6_ECOD1]] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity).[HAMAP-Rule:MF_01470]
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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/nk/3nkd_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=3nkd 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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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses and plasmids in prokaryotes. Cas1 is a CRISPR-associated protein that is common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show that the purified Cas1 protein of Escherichia coli (YgbT) exhibits nuclease activity against single-stranded and branched DNAs including Holliday junctions, replication forks and 5'-flaps. The crystal structure of YgbT and site-directed mutagenesis have revealed the potential active site. Genome-wide screens show that YgbT physically and genetically interacts with key components of DNA repair systems, including recB, recC and ruvB. Consistent with these findings, the ygbT deletion strain showed increased sensitivity to DNA damage and impaired chromosomal segregation. Similar phenotypes were observed in strains with deletion of CRISPR clusters, suggesting that the function of YgbT in repair involves interaction with the CRISPRs. These results show that YgbT belongs to a novel, structurally distinct family of nucleases acting on branched DNAs and suggest that, in addition to antiviral immunity, at least some components of the CRISPR-Cas system have a function in DNA repair.
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===Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12===
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A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair.,Babu M, Beloglazova N, Flick R, Graham C, Skarina T, Nocek B, Gagarinova A, Pogoutse O, Brown G, Binkowski A, Phanse S, Joachimiak A, Koonin EV, Savchenko A, Emili A, Greenblatt J, Edwards AM, Yakunin AF Mol Microbiol. 2011 Jan;79(2):484-502. doi:, 10.1111/j.1365-2958.2010.07465.x. Epub 2010 Dec 7. PMID:21219465<ref>PMID:21219465</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3nkd" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_21219465}}, adds the Publication Abstract to the page
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*[[Endonuclease|Endonuclease]]
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(as it appears on PubMed at http://www.pubmed.gov), where 21219465 is the PubMed ID number.
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== References ==
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-->
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<references/>
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{{ABSTRACT_PUBMED_21219465}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Ecod1]]
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[[3nkd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NKD OCA].
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[[Category: Beloglazova, N]]
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[[Category: Joachimiak, A]]
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==Reference==
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[[Category: Nocek, B]]
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<ref group="xtra">PMID:21219465</ref><references group="xtra"/>
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[[Category: Savchenko, A]]
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[[Category: Escherichia coli]]
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[[Category: Skarina, T]]
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[[Category: Beloglazova, N.]]
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[[Category: Yakunin, A]]
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[[Category: Joachimiak, A.]]
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[[Category: Cas1]]
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[[Category: Nocek, B.]]
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[[Category: Crispr]]
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[[Category: Savchenko, A.]]
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[[Category: Dna recombination]]
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[[Category: Skarina, T.]]
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[[Category: Dna repair]]
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[[Category: Yakunin, A.]]
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[[Category: Immune system]]
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[[Category: Nuclease]]
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[[Category: Ygbt]]

Current revision

Structure of CRISP-associated protein Cas1 from Escherichia coli str. K-12

3nkd, resolution 1.95Å

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