5kk5

From Proteopedia

(Difference between revisions)

Revision as of 10:48, 27 September 2023

AsCpf1(E993A)-crRNA-DNA ternary complex

Structural highlights

5kk5 is a 4 chain structure with sequence from Acidaminococcus sp. BV3L6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.289Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CS12A_ACISB 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). Recognizes a short motif in the CRISPR repeat sequences (the 5' PAM or protospacer adjacent motif, TTTN in this organism) to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs (PubMed:26422227). Has dsDNA endonuclease activity, results in staggered 4-base 5' overhangs 19 and 22 bases downstream of the PAM on the non-targeted and targeted strand respectively (PubMed:26422227). Non-target strand cleavage by the RuvC domain is probably a prerequisite of target strand cleavage by the Nuc domain (PubMed:27114038). In this CRISPR system correct processing of pre-crRNA requires only this protein and the CRISPR locus (By similarity).[UniProtKB:A0Q7Q2]^[1] ^[2]

Publication Abstract from PubMed

CRISPR-Cas9 and CRISPR-Cpf1 systems have been successfully harnessed for genome editing. In the CRISPR-Cas9 system, the preordered A-form RNA seed sequence and preformed protein PAM-interacting cleft are essential for Cas9 to form a DNA recognition-competent structure. Whether the CRISPR-Cpf1 system employs a similar mechanism for target DNA recognition remains unclear. Here, we have determined the crystal structure of Acidaminococcus sp. Cpf1 (AsCpf1) in complex with crRNA and target DNA. Structural comparison between the AsCpf1-crRNA-DNA ternary complex and the recently reported Lachnospiraceae bacterium Cpf1 (LbCpf1)-crRNA binary complex identifies a unique mechanism employed by Cpf1 for target recognition. The seed sequence required for initial DNA interrogation is disordered in the Cpf1-cRNA binary complex, but becomes ordered upon ternary complex formation. Further, the PAM interacting cleft of Cpf1 undergoes an "open-to-closed" conformational change upon target DNA binding, which in turn induces structural changes within Cpf1 to accommodate the ordered A-form seed RNA segment. This unique mechanism of target recognition by Cpf1 is distinct from that reported previously for Cas9.

Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition.,Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ Cell Res. 2016 Aug;26(8):901-13. doi: 10.1038/cr.2016.88. Epub 2016 Jul 22. PMID:27444870^[3]

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

References

↑ Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell. 2015 Oct 22;163(3):759-71. doi: 10.1016/j.cell.2015.09.038. Epub 2015 Sep, 25. PMID:26422227 doi:http://dx.doi.org/10.1016/j.cell.2015.09.038
↑ Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O. Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. Cell. 2016 May 5;165(4):949-62. doi: 10.1016/j.cell.2016.04.003. Epub 2016 Apr, 21. PMID:27114038 doi:http://dx.doi.org/10.1016/j.cell.2016.04.003
↑ Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Cell Res. 2016 Aug;26(8):901-13. doi: 10.1038/cr.2016.88. Epub 2016 Jul 22. PMID:27444870 doi:http://dx.doi.org/10.1038/cr.2016.88

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/5kk5"

@@ Line 3: / Line 3: @@
 <StructureSection load='5kk5' size='340' side='right'caption='[[5kk5]], [[Resolution|resolution]] 3.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5kk5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KK5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KK5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5kk5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidaminococcus_sp._BV3L6 Acidaminococcus sp. BV3L6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KK5 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5kk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kk5 OCA], [http://pdbe.org/5kk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kk5 RCSB], [http://www.ebi.ac.uk/pdbsum/5kk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kk5 ProSAT]</span></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]] 3.289&#8491;</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=5kk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kk5 OCA], [https://pdbe.org/5kk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kk5 RCSB], [https://www.ebi.ac.uk/pdbsum/5kk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kk5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CPF1_ACISB CPF1_ACISB]] 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). Has dsDNA endonuclease activity, results in a 4-base 5' overhang 19 and 22 bases downstream of the PAM on the non-targeted and targeted strand respectively (PubMed:26422227). In this CRISPR system correct processing of pre-crRNA requires only this protein and the CRISPR locus (By similarity).[UniProtKB:A0Q7Q2]<ref>PMID:26422227</ref>
+[https://www.uniprot.org/uniprot/CS12A_ACISB CS12A_ACISB] 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). Recognizes a short motif in the CRISPR repeat sequences (the 5' PAM or protospacer adjacent motif, TTTN in this organism) to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs (PubMed:26422227). Has dsDNA endonuclease activity, results in staggered 4-base 5' overhangs 19 and 22 bases downstream of the PAM on the non-targeted and targeted strand respectively (PubMed:26422227). Non-target strand cleavage by the RuvC domain is probably a prerequisite of target strand cleavage by the Nuc domain (PubMed:27114038). In this CRISPR system correct processing of pre-crRNA requires only this protein and the CRISPR locus (By similarity).[UniProtKB:A0Q7Q2]<ref>PMID:26422227</ref> <ref>PMID:27114038</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 27: @@
 __TOC__
 </StructureSection>
+[[Category: Acidaminococcus sp. BV3L6]]
 [[Category: Large Structures]]
-[[Category: Gao, P]]
+[[Category: Gao P]]
-[[Category: Huang, Z]]
+[[Category: Huang Z]]
-[[Category: Patel, D J]]
+[[Category: Patel DJ]]
-[[Category: Rajashankar, K R]]
+[[Category: Rajashankar KR]]
-[[Category: Yang, H]]
+[[Category: Yang H]]
-[[Category: Cpf1]]
-[[Category: Crispr-ca]]
-[[Category: Crrna]]
-[[Category: Hydrolase-dna-rna complex]]

5kk5

From Proteopedia

Revision as of 10:48, 27 September 2023

AsCpf1(E993A)-crRNA-DNA ternary complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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