5ux0

From Proteopedia

(Difference between revisions)

Current revision

X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA

Structural highlights

5ux0 is a 6 chain structure with sequence from Marinitoga piezophila and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.197Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGO_MARPK An RNA-guided ssDNA endonuclease that may play a role in defense against invading mobile genetic elements. Uses short 5'-OH-ssRNA sequences as guides (gRNA) to bind complementary target DNA (tDNA) or target RNA resulting in target cleavage. The cleavage site is 10 nucleotides (nt) downstream of the target residue base-paired with the 5'-end of the gRNA. Reaction rates are fastest on 5'-OH-gRNA:tDNA followed by 5'-OH-gRNA:target RNA. gRNA between 17-21 nt supports equivalent rates of cleavage, has no preferred 5'-nt. Has weak activity on tDNA with 5'-phospho-gRNA, yielding products 1-2 nt longer (PubMed:27035975). Unlike other characterized prokaryotic Ago proteins symmetric mismatches centered around the cleavage site reduce cleavage efficiency (PubMed:28520746).^[1] ^[2]

Publication Abstract from PubMed

Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5'-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 A resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate. Comparison of this ternary complex to other target-bound Argonaute structures reveals a unique orientation of the N-terminal domain, resulting in a straight helical axis of the entire RNA-DNA heteroduplex through the central cleft of the protein. Additionally, mismatches introduced into the heteroduplex reduce MpAgo cleavage efficiency with a symmetric profile centered around the middle of the helix. This pattern differs from the canonical mismatch tolerance of other Argonautes, which display decreased cleavage efficiency for substrates bearing sequence mismatches to the 5' region of the guide strand. This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins.

DNA recognition by an RNA-guided bacterial Argonaute.,Doxzen KW, Doudna JA PLoS One. 2017 May 17;12(5):e0177097. doi: 10.1371/journal.pone.0177097., eCollection 2017. PMID:28520746^[3]

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

References

↑ Kaya E, Doxzen KW, Knoll KR, Wilson RC, Strutt SC, Kranzusch PJ, Doudna JA. A bacterial Argonaute with noncanonical guide RNA specificity. Proc Natl Acad Sci U S A. 2016 Mar 30. pii: 201524385. PMID:27035975 doi:http://dx.doi.org/10.1073/pnas.1524385113
↑ Doxzen KW, Doudna JA. DNA recognition by an RNA-guided bacterial Argonaute. PLoS One. 2017 May 17;12(5):e0177097. doi: 10.1371/journal.pone.0177097., eCollection 2017. PMID:28520746 doi:http://dx.doi.org/10.1371/journal.pone.0177097
↑ Doxzen KW, Doudna JA. DNA recognition by an RNA-guided bacterial Argonaute. PLoS One. 2017 May 17;12(5):e0177097. doi: 10.1371/journal.pone.0177097., eCollection 2017. PMID:28520746 doi:http://dx.doi.org/10.1371/journal.pone.0177097

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/5ux0"

Categories: Large Structures | Marinitoga piezophila | Synthetic construct | Doudna JA | Doxzen KW

@@ Line 1: / Line 1: @@
 ==X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA==
-<StructureSection load='5ux0' size='340' side='right' caption='[[5ux0]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='5ux0' size='340' side='right'caption='[[5ux0]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ux0]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UX0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UX0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ux0]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Marinitoga_piezophila Marinitoga piezophila] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UX0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UX0 FirstGlance]. <br>
-</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=5ux0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ux0 OCA], [http://pdbe.org/5ux0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ux0 RCSB], [http://www.ebi.ac.uk/pdbsum/5ux0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ux0 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]] 3.197&#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=5ux0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ux0 OCA], [https://pdbe.org/5ux0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ux0 RCSB], [https://www.ebi.ac.uk/pdbsum/5ux0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ux0 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AGO_MARPK AGO_MARPK] An RNA-guided ssDNA endonuclease that may play a role in defense against invading mobile genetic elements. Uses short 5'-OH-ssRNA sequences as guides (gRNA) to bind complementary target DNA (tDNA) or target RNA resulting in target cleavage. The cleavage site is 10 nucleotides (nt) downstream of the target residue base-paired with the 5'-end of the gRNA. Reaction rates are fastest on 5'-OH-gRNA:tDNA followed by 5'-OH-gRNA:target RNA. gRNA between 17-21 nt supports equivalent rates of cleavage, has no preferred 5'-nt. Has weak activity on tDNA with 5'-phospho-gRNA, yielding products 1-2 nt longer (PubMed:27035975). Unlike other characterized prokaryotic Ago proteins symmetric mismatches centered around the cleavage site reduce cleavage efficiency (PubMed:28520746).<ref>PMID:27035975</ref> <ref>PMID:28520746</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 </div>
 <div class="pdbe-citations 5ux0" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Argonaute 3D structures|Argonaute 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Doudna, J A]]
+[[Category: Large Structures]]
-[[Category: Doxzen, K W]]
+[[Category: Marinitoga piezophila]]
-[[Category: Argonaute]]
+[[Category: Synthetic construct]]
-[[Category: Dna]]
+[[Category: Doudna JA]]
-[[Category: Hydrolase-rna-dna complex]]
+[[Category: Doxzen KW]]
-[[Category: Rna]]
-[[Category: Rnai]]

5ux0

From Proteopedia

Current revision

X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox