6o56

From Proteopedia

(Difference between revisions)

Revision as of 16:40, 22 January 2020

HNH Nuclease from S. pyogenes Cas9

Structural highlights

6o56 is a 2 chain structure with sequence from Strp1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Gene:	cas9, csn1, SPy_1046 (STRP1)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CAS9_STRP1] 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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) (Probable). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed by 3'-5' exonucleolytically. DNA-binding requires protein and both RNA species. Cas9 probably recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus nonself.^[1] ^[2]

Publication Abstract from PubMed

CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian-accelerated molecular dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond time scale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome-editing capability.

Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics.,East KW, Newton JC, Morzan UN, Narkhede YB, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP J Am Chem Soc. 2020 Jan 9. doi: 10.1021/jacs.9b10521. PMID:31885264^[3]

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

References

↑ Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature. 2011 Mar 31;471(7340):602-7. doi: 10.1038/nature09886. PMID:21455174 doi:http://dx.doi.org/10.1038/nature09886
↑ Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012 Aug 17;337(6096):816-21. doi: 10.1126/science.1225829. Epub 2012, Jun 28. PMID:22745249 doi:http://dx.doi.org/10.1126/science.1225829
↑ East KW, Newton JC, Morzan UN, Narkhede YB, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP. Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics. J Am Chem Soc. 2020 Jan 9. doi: 10.1021/jacs.9b10521. PMID:31885264 doi:http://dx.doi.org/10.1021/jacs.9b10521

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/6o56"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6o56 is ON HOLD  until Paper Publication
+==HNH Nuclease from S. pyogenes Cas9==
+<StructureSection load='6o56' size='340' side='right'caption='[[6o56]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6o56]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strp1 Strp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O56 FirstGlance]. <br>
+</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cas9, csn1, SPy_1046 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=301447 STRP1])</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=6o56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o56 OCA], [http://pdbe.org/6o56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o56 RCSB], [http://www.ebi.ac.uk/pdbsum/6o56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o56 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/CAS9_STRP1 CAS9_STRP1]] 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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) (Probable). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed by 3'-5' exonucleolytically. DNA-binding requires protein and both RNA species. Cas9 probably recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus nonself.<ref>PMID:21455174</ref> <ref>PMID:22745249</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+CRISPR-Cas9 is a widely employed genome-editing tool with functionality reliant on the ability of the Cas9 endonuclease to introduce site-specific breaks in double-stranded DNA. In this system, an intriguing allosteric communication has been suggested to control its DNA cleavage activity through flexibility of the catalytic HNH domain. Here, solution NMR experiments and a novel Gaussian-accelerated molecular dynamics (GaMD) simulation method are used to capture the structural and dynamic determinants of allosteric signaling within the HNH domain. We reveal the existence of a millisecond time scale dynamic pathway that spans HNH from the region interfacing the adjacent RuvC nuclease and propagates up to the DNA recognition lobe in full-length CRISPR-Cas9. These findings reveal a potential route of signal transduction within the CRISPR-Cas9 HNH nuclease, advancing our understanding of the allosteric pathway of activation. Further, considering the role of allosteric signaling in the specificity of CRISPR-Cas9, this work poses the mechanistic basis for novel engineering efforts aimed at improving its genome-editing capability.
-Authors: Newton, J.C., Lisi, G.P., Jogl, G.
+Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics.,East KW, Newton JC, Morzan UN, Narkhede YB, Acharya A, Skeens E, Jogl G, Batista VS, Palermo G, Lisi GP J Am Chem Soc. 2020 Jan 9. doi: 10.1021/jacs.9b10521. PMID:31885264<ref>PMID:31885264</ref>
-Description: HNH Nuclease from S. pyogenes Cas9
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Newton, J.C]]
+<div class="pdbe-citations 6o56" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Strp1]]
 [[Category: Jogl, G]]
-[[Category: Lisi, G.P]]
+[[Category: Lisi, G P]]
+[[Category: Newton, J C]]
+[[Category: Crispr cas9]]
+[[Category: Dna binding protein]]
+[[Category: Nuclease]]

6o56

From Proteopedia

Revision as of 16:40, 22 January 2020

HNH Nuclease from S. pyogenes Cas9

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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