5dqz

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Revision as of 14:12, 16 November 2017

Crystal Structure of Cas-DNA-PAM complex

Structural highlights

5dqz is a 8 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	5dlj, 5dqu, 5dqt
Gene:	ygbT, cas1, b2755, JW2725 (ECOLI), ygbF, cas2, b2754, JW5438 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CAS2_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). Functions as a ssRNA-specific endoribonuclease (By similarity).^[1] [CAS1_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). Cas1 is thought to be involved in CRISPR adaptation, the first stage of CRISPR immunity. Might be involved in the addition/removal of CRISPR spacers. Endonucleolytically cleaves linear ssRNA, ssDNA and short (34 base) dsDNA as well as branched DNA substrates such as Holliday junctions, replication forks and 5'-flap DNA substrates. Genetic interactions suggest Cas1 interacts with components of the RecBC and RuvB DNA repair systems.^[2]

Publication Abstract from PubMed

Bacteria acquire memory of viral invaders by incorporating invasive DNA sequence elements into the host CRISPR locus, generating a new spacer within the CRISPR array. We report on the structures of Cas1-Cas2-dual-forked DNA complexes in an effort toward understanding how the protospacer is sampled prior to insertion into the CRISPR locus. Our study reveals a protospacer DNA comprising a 23-bp duplex bracketed by tyrosine residues, together with anchored flanking 3' overhang segments. The PAM-complementary sequence in the 3' overhang is recognized by the Cas1a catalytic subunits in a base-specific manner, and subsequent cleavage at positions 5 nt from the duplex boundary generates a 33-nt DNA intermediate that is incorporated into the CRISPR array via a cut-and-paste mechanism. Upon protospacer binding, Cas1-Cas2 undergoes a significant conformational change, generating a flat surface conducive to proper protospacer recognition. Here, our study provides important structure-based mechanistic insights into PAM-dependent spacer acquisition.

Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems.,Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y Cell. 2015 Nov 5;163(4):840-53. doi: 10.1016/j.cell.2015.10.008. Epub 2015 Oct, 17. PMID:26478180^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ 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
↑ Wang J, Li J, Zhao H, Sheng G, Wang M, Yin M, Wang Y. Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems. Cell. 2015 Nov 5;163(4):840-53. doi: 10.1016/j.cell.2015.10.008. Epub 2015 Oct, 17. PMID:26478180 doi:http://dx.doi.org/10.1016/j.cell.2015.10.008

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5dqz"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Cas-DNA-PAM complex==
 <StructureSection load='5dqz' size='340' side='right' caption='[[5dqz]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5dqz]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DQZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5dqz]] is a 8 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=5DQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DQZ FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5dlj|5dlj]], [[5dqu|5dqu]], [[5dqt|5dqt]]</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=5dqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dqz OCA], [http://pdbe.org/5dqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dqz RCSB], [http://www.ebi.ac.uk/pdbsum/5dqz PDBsum]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ygbT, cas1, b2755, JW2725 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), ygbF, cas2, b2754, JW5438 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5dqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dqz OCA], [http://pdbe.org/5dqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dqz RCSB], [http://www.ebi.ac.uk/pdbsum/5dqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dqz ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 22: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Ecoli]]
 [[Category: Li, J]]
 [[Category: Sheng, G]]

5dqz

From Proteopedia

Revision as of 14:12, 16 November 2017

Crystal Structure of Cas-DNA-PAM complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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