5ds4

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA

Structural highlights

5ds4 is a 8 chain structure with sequence from Escherichia coli K-12 and Escherichia virus M13. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
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]

Publication Abstract from PubMed

Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (CRISPR) loci as spacer segments. The universally conserved Cas1-Cas2 integrase complex catalyses spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases. How the Cas1-Cas2 complex selects foreign DNA substrates for integration remains unknown. Here we present X-ray crystal structures of the Escherichia coli Cas1-Cas2 complex bound to cognate 33-nucleotide protospacer DNA substrates. The protein complex creates a curved binding surface spanning the length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3'-OH to enter a channel leading into the Cas1 active sites. Phosphodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspecific substrate selection observed in vivo. Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1-Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci.

Foreign DNA capture during CRISPR-Cas adaptive immunity.,Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA Nature. 2015 Nov 26;527(7579):535-8. doi: 10.1038/nature15760. Epub 2015 Oct 21. PMID:26503043^[2]

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
↑ Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA. Foreign DNA capture during CRISPR-Cas adaptive immunity. Nature. 2015 Nov 26;527(7579):535-8. doi: 10.1038/nature15760. Epub 2015 Oct 21. PMID:26503043 doi:http://dx.doi.org/10.1038/nature15760

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ds4"

@@ Line 1: / Line 1: @@
 ==Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA==
-<StructureSection load='5ds4' size='340' side='right' caption='[[5ds4]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='5ds4' size='340' side='right'caption='[[5ds4]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ds4]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ds4]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_virus_M13 Escherichia virus M13]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DS4 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4p6i|4p6i]]</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]] 3.2&#8491;</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=5ds4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds4 OCA], [http://pdbe.org/5ds4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds4 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds4 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=5ds4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds4 OCA], [https://pdbe.org/5ds4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ds4 RCSB], [https://www.ebi.ac.uk/pdbsum/5ds4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CAS1_ECOLI 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.<ref>PMID:21255106</ref>  [[http://www.uniprot.org/uniprot/CAS2_ECOLI 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).<ref>PMID:21255106</ref>
+[https://www.uniprot.org/uniprot/CAS2_ECOLI 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).<ref>PMID:21255106</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 5ds4" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Doudna, J A]]
+[[Category: Escherichia coli K-12]]
-[[Category: Engelman, A N]]
+[[Category: Escherichia virus M13]]
-[[Category: Harrington, L B]]
+[[Category: Large Structures]]
-[[Category: Kranzusch, P J]]
+[[Category: Doudna JA]]
-[[Category: Nunez, J K]]
+[[Category: Engelman AN]]
-[[Category: Clustered regularly interspaced short palindromic repeat]]
+[[Category: Harrington LB]]
-[[Category: Crispr-cas system]]
+[[Category: Kranzusch PJ]]
-[[Category: Dna binding protein]]
+[[Category: Nunez JK]]
-[[Category: Endodeoxyribonuclease]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase-dna complex]]
-[[Category: Integrase]]

5ds4

From Proteopedia

Current revision

Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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