4uw2

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Csm1 in T.onnurineus

Structural highlights

4uw2 is a 4 chain structure with sequence from Thermococcus onnurineus NA1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAS10_THEON 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). The type III-A Csm effector complex binds crRNA and acts as a crRNA-guided RNase, DNase and cyclic oligoadenylate synthase; binding of target RNA cognate to the crRNA is required for all activities.[UniProtKB:A0A0A7HFE1] A single-strand deoxyribonuclease (ssDNase) which digests linear and circular ssDNA; has 5'-3' and 3'-5' exonuclease activity as well as a less efficient endonuclease activity. Has a minimal size requirement; 100 nucleotide ssDNA (nt) is more efficiently digested than 50 or 25 nt ssDNA, while 14 nt ssDNA is not cleaved at all. It has no activity on dsDNA or ssRNA.^[1] ssDNase activity is stimulated in the ternary Csm effector complex; binding of cognate target RNA activates the ssDNase, as the target RNA is degraded ssDNA activity decreases.[UniProtKB:A0A0A7HFE1] When associated with the ternary Csm effector complex (the crRNA, Cas proteins and a cognate target ssRNA) synthesizes cyclic oligoadenylates (cOA) from ATP. cOAs are second messengers that stimulate the ssRNase activity of Csm6, inducing an antiviral state important for defense against invading nucleic acids.[UniProtKB:A0A0A7HFE1]

Publication Abstract from PubMed

The CRISPR-Cas system is the RNA-guided immune defense mechanism in bacteria and archaea. Csm1 belongs to the Cas10 family, which is the common signature protein of the type III system. Csm1 is the largest subunit of the Csm interference complex in the type III-A subtype, which targets foreign DNA or RNA. Here, we report crystallographic and biochemical analyses of Thermococcus onnurineus Csm1, revealing a five-domain organization and single-stranded DNA (ssDNA)-specific nuclease activity associated with the N-terminal HD domain. This domain folds into permuted secondary structures in comparison with the HD domain of Cas3 and contains all the catalytically important residues. It exhibited both endo- and exonuclease activities in an Ni2+ or Mn2+-dependent manner. The narrow width of the active-site cleft appears to restrict the substrate specificity to ssDNA and thus to prevent Csm1 from cleaving double-stranded chromosomal DNA. These data suggest that Csm1 may function in DNA interference by the Csm effector complex.

Crystal Structure of the Csm1 Subunit of the Csm Complex and Its Single-Stranded DNA-Specific Nuclease Activity.,Jung TY, An Y, Park KH, Lee MH, Oh BH, Woo E Structure. 2015 Mar 3. pii: S0969-2126(15)00045-3. doi:, 10.1016/j.str.2015.01.021. PMID:25773141^[2]

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

References

↑ Jung TY, An Y, Park KH, Lee MH, Oh BH, Woo E. Crystal Structure of the Csm1 Subunit of the Csm Complex and Its Single-Stranded DNA-Specific Nuclease Activity. Structure. 2015 Mar 3. pii: S0969-2126(15)00045-3. doi:, 10.1016/j.str.2015.01.021. PMID:25773141 doi:http://dx.doi.org/10.1016/j.str.2015.01.021
↑ Jung TY, An Y, Park KH, Lee MH, Oh BH, Woo E. Crystal Structure of the Csm1 Subunit of the Csm Complex and Its Single-Stranded DNA-Specific Nuclease Activity. Structure. 2015 Mar 3. pii: S0969-2126(15)00045-3. doi:, 10.1016/j.str.2015.01.021. PMID:25773141 doi:http://dx.doi.org/10.1016/j.str.2015.01.021

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/4uw2"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 4uw2 is ON HOLD  until Paper Publication
+==Crystal structure of Csm1 in T.onnurineus==
+<StructureSection load='4uw2' size='340' side='right'caption='[[4uw2]], [[Resolution|resolution]] 2.63&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4uw2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_onnurineus_NA1 Thermococcus onnurineus NA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UW2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UW2 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=4uw2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uw2 OCA], [https://pdbe.org/4uw2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uw2 RCSB], [https://www.ebi.ac.uk/pdbsum/4uw2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uw2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAS10_THEON CAS10_THEON] 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). The type III-A Csm effector complex binds crRNA and acts as a crRNA-guided RNase, DNase and cyclic oligoadenylate synthase; binding of target RNA cognate to the crRNA is required for all activities.[UniProtKB:A0A0A7HFE1]  A single-strand deoxyribonuclease (ssDNase) which digests linear and circular ssDNA; has 5'-3' and 3'-5' exonuclease activity as well as a less efficient endonuclease activity. Has a minimal size requirement; 100 nucleotide ssDNA (nt) is more efficiently digested than 50 or 25 nt ssDNA, while 14 nt ssDNA is not cleaved at all. It has no activity on dsDNA or ssRNA.<ref>PMID:25773141</ref>   ssDNase activity is stimulated in the ternary Csm effector complex; binding of cognate target RNA activates the ssDNase, as the target RNA is degraded ssDNA activity decreases.[UniProtKB:A0A0A7HFE1]  When associated with the ternary Csm effector complex (the crRNA, Cas proteins and a cognate target ssRNA) synthesizes cyclic oligoadenylates (cOA) from ATP. cOAs are second messengers that stimulate the ssRNase activity of Csm6, inducing an antiviral state important for defense against invading nucleic acids.[UniProtKB:A0A0A7HFE1]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The CRISPR-Cas system is the RNA-guided immune defense mechanism in bacteria and archaea. Csm1 belongs to the Cas10 family, which is the common signature protein of the type III system. Csm1 is the largest subunit of the Csm interference complex in the type III-A subtype, which targets foreign DNA or RNA. Here, we report crystallographic and biochemical analyses of Thermococcus onnurineus Csm1, revealing a five-domain organization and single-stranded DNA (ssDNA)-specific nuclease activity associated with the N-terminal HD domain. This domain folds into permuted secondary structures in comparison with the HD domain of Cas3 and contains all the catalytically important residues. It exhibited both endo- and exonuclease activities in an Ni2+ or Mn2+-dependent manner. The narrow width of the active-site cleft appears to restrict the substrate specificity to ssDNA and thus to prevent Csm1 from cleaving double-stranded chromosomal DNA. These data suggest that Csm1 may function in DNA interference by the Csm effector complex.
-Authors: Jung, T.Y., An, Y., Park, K.H., Lee, M.H., Oh, B.H., Woo, E.J.
+Crystal Structure of the Csm1 Subunit of the Csm Complex and Its Single-Stranded DNA-Specific Nuclease Activity.,Jung TY, An Y, Park KH, Lee MH, Oh BH, Woo E Structure. 2015 Mar 3. pii: S0969-2126(15)00045-3. doi:, 10.1016/j.str.2015.01.021. PMID:25773141<ref>PMID:25773141</ref>
-Description: Crystal structure of Csm1 in T.onnurineus
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: An, Y]]
+<div class="pdbe-citations 4uw2" style="background-color:#fffaf0;"></div>
-[[Category: Oh, B.H]]
+== References ==
-[[Category: Jung, T.Y]]
+<references/>
-[[Category: Park, K.H]]
+__TOC__
-[[Category: Woo, E.J]]
+</StructureSection>
-[[Category: Lee, M.H]]
+[[Category: Large Structures]]
+[[Category: Thermococcus onnurineus NA1]]
+[[Category: An Y]]
+[[Category: Jung TY]]
+[[Category: Lee MH]]
+[[Category: Oh BH]]
+[[Category: Park KH]]
+[[Category: Woo EJ]]

4uw2

From Proteopedia

Current revision

Crystal structure of Csm1 in T.onnurineus

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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