4dzd

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the CRISPR-associated protein Cas6e from Escherichia coli str. K-12

Structural highlights

4dzd is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.999Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAS6_ECOLI 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).^[1] ^[2] ^[3] ^[4] ^[5] CasE is required to process the pre-crRNA into single repeat-spacer units, with an 8-nt 5'-repeat DNA tag that may help other proteins recognize the crRNA. This subunit alone will cleave pre-crRNA, as will CasCDE or CasCE; cleavage does not require divalent metals or ATP. CasCDE alone is also able to form R-loops. Partially inhibits the cleavage of Holliday junctions by YgbT (Cas1). Yields a 5'-hydroxy group and a 2',3'-cyclic phosphate terminus.^[6] ^[7] ^[8] ^[9] ^[10] A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization.^[11] ^[12] ^[13] ^[14] ^[15]

References

↑ Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008 Aug 15;321(5891):960-4. doi: 10.1126/science.1159689. PMID:18703739 doi:http://dx.doi.org/10.1126/science.1159689
↑ 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. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol. 2011 Jan;79(2):484-502. doi:, 10.1111/j.1365-2958.2010.07465.x. Epub 2010 Dec 7. PMID:21219465 doi:10.1111/j.1365-2958.2010.07465.x
↑ Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke A, DeLisa MP. Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli. Mol Microbiol. 2011 Feb;79(3):584-99. doi: 10.1111/j.1365-2958.2010.07482.x. Epub, 2010 Dec 13. PMID:21255106 doi:10.1111/j.1365-2958.2010.07482.x
↑ Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011 May;18(5):529-36. doi: 10.1038/nsmb.2019. Epub 2011 Apr, 3. PMID:21460843 doi:http://dx.doi.org/10.1038/nsmb.2019
↑ Howard JA, Delmas S, Ivancic-Bace I, Bolt EL. Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein. Biochem J. 2011 Oct 1;439(1):85-95. doi: 10.1042/BJ20110901. PMID:21699496 doi:http://dx.doi.org/10.1042/BJ20110901
↑ Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008 Aug 15;321(5891):960-4. doi: 10.1126/science.1159689. PMID:18703739 doi:http://dx.doi.org/10.1126/science.1159689
↑ 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. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol. 2011 Jan;79(2):484-502. doi:, 10.1111/j.1365-2958.2010.07465.x. Epub 2010 Dec 7. PMID:21219465 doi:10.1111/j.1365-2958.2010.07465.x
↑ Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke A, DeLisa MP. Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli. Mol Microbiol. 2011 Feb;79(3):584-99. doi: 10.1111/j.1365-2958.2010.07482.x. Epub, 2010 Dec 13. PMID:21255106 doi:10.1111/j.1365-2958.2010.07482.x
↑ Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011 May;18(5):529-36. doi: 10.1038/nsmb.2019. Epub 2011 Apr, 3. PMID:21460843 doi:http://dx.doi.org/10.1038/nsmb.2019
↑ Howard JA, Delmas S, Ivancic-Bace I, Bolt EL. Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein. Biochem J. 2011 Oct 1;439(1):85-95. doi: 10.1042/BJ20110901. PMID:21699496 doi:http://dx.doi.org/10.1042/BJ20110901
↑ Brouns SJ, Jore MM, Lundgren M, Westra ER, Slijkhuis RJ, Snijders AP, Dickman MJ, Makarova KS, Koonin EV, van der Oost J. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science. 2008 Aug 15;321(5891):960-4. doi: 10.1126/science.1159689. PMID:18703739 doi:http://dx.doi.org/10.1126/science.1159689
↑ 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. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol. 2011 Jan;79(2):484-502. doi:, 10.1111/j.1365-2958.2010.07465.x. Epub 2010 Dec 7. PMID:21219465 doi:10.1111/j.1365-2958.2010.07465.x
↑ Perez-Rodriguez R, Haitjema C, Huang Q, Nam KH, Bernardis S, Ke A, DeLisa MP. Envelope stress is a trigger of CRISPR RNA-mediated DNA silencing in Escherichia coli. Mol Microbiol. 2011 Feb;79(3):584-99. doi: 10.1111/j.1365-2958.2010.07482.x. Epub, 2010 Dec 13. PMID:21255106 doi:10.1111/j.1365-2958.2010.07482.x
↑ Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ. Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat Struct Mol Biol. 2011 May;18(5):529-36. doi: 10.1038/nsmb.2019. Epub 2011 Apr, 3. PMID:21460843 doi:http://dx.doi.org/10.1038/nsmb.2019
↑ Howard JA, Delmas S, Ivancic-Bace I, Bolt EL. Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein. Biochem J. 2011 Oct 1;439(1):85-95. doi: 10.1042/BJ20110901. PMID:21699496 doi:http://dx.doi.org/10.1042/BJ20110901

1 Structural highlights
2 Function
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4dzd"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the CRISPR-associated protein Cas6e from Escherichia coli str. K-12==
-<StructureSection load='4dzd' size='340' side='right' caption='[[4dzd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='4dzd' size='340' side='right'caption='[[4dzd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4dzd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DZD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4dzd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DZD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.999&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ygcH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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></td></tr>
-<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=4dzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dzd OCA], [http://pdbe.org/4dzd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dzd RCSB], [http://www.ebi.ac.uk/pdbsum/4dzd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dzd 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=4dzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dzd OCA], [https://pdbe.org/4dzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dzd RCSB], [https://www.ebi.ac.uk/pdbsum/4dzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dzd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CAS6_ECOLI CAS6_ECOLI]] 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).<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref>   CasE is required to process the pre-crRNA into single repeat-spacer units, with an 8-nt 5'-repeat DNA tag that may help other proteins recognize the crRNA. This subunit alone will cleave pre-crRNA, as will CasCDE or CasCE; cleavage does not require divalent metals or ATP. CasCDE alone is also able to form R-loops. Partially inhibits the cleavage of Holliday junctions by YgbT (Cas1). Yields a 5'-hydroxy group and a 2',3'-cyclic phosphate terminus.<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref>   A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization.<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref>
+[https://www.uniprot.org/uniprot/CAS6_ECOLI CAS6_ECOLI] 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).<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref>   CasE is required to process the pre-crRNA into single repeat-spacer units, with an 8-nt 5'-repeat DNA tag that may help other proteins recognize the crRNA. This subunit alone will cleave pre-crRNA, as will CasCDE or CasCE; cleavage does not require divalent metals or ATP. CasCDE alone is also able to form R-loops. Partially inhibits the cleavage of Holliday junctions by YgbT (Cas1). Yields a 5'-hydroxy group and a 2',3'-cyclic phosphate terminus.<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref>   A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization.<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref>
 ==See Also==
 *[[CRISPR type I-E (Cascade)|CRISPR type I-E (Cascade)]]
-*[[Endonuclease|Endonuclease]]
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Gong, W]]
+[[Category: Large Structures]]
-[[Category: Huang, G]]
+[[Category: Gong W]]
-[[Category: Wang, Y]]
+[[Category: Huang G]]
-[[Category: Wei, J]]
+[[Category: Wang Y]]
-[[Category: Crrna]]
+[[Category: Wei J]]
-[[Category: Endoribonuclease]]
-[[Category: Ferredoxin-like domain]]
-[[Category: Hydrolase]]

4dzd

From Proteopedia

Current revision

Crystal structure of the CRISPR-associated protein Cas6e from Escherichia coli str. K-12

Structural highlights

Function

See Also

References

Contents

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