5g5t: Difference between revisions
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==Structure of the Argonaute protein from Methanocaldcoccus janaschii in complex with guide DNA== | ==Structure of the Argonaute protein from Methanocaldcoccus janaschii in complex with guide DNA== | ||
<StructureSection load='5g5t' size='340' side='right' caption='[[5g5t]], [[Resolution|resolution]] 2.85Å' scene=''> | <StructureSection load='5g5t' size='340' side='right'caption='[[5g5t]], [[Resolution|resolution]] 2.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5g5t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G5T OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5g5t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5G5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5G5T FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5g5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5g5t OCA], [https://pdbe.org/5g5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5g5t RCSB], [https://www.ebi.ac.uk/pdbsum/5g5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5g5t ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/AGO_METJA AGO_METJA] A DNA-guided ssDNA endonuclease that may play a role in defense against invading genetic elements. Uses short ssDNA sequences as guides (gDNA) to bind complementary target strands, resulting in slicing of the target DNA (tDNA) (PubMed:24442234, PubMed:27741323, PubMed:28319081, PubMed:28319084). Endonucleolytically cleaves tDNA (the gDNA indicates where to cleave); two major and two minor products are seen which correspond to cleavage sites between nucleotides 9/10, 10/11, 13/14, and 14/15 downstream of the target residue base-paired with the 5'-end of the gDNA (PubMed:24442234, PubMed:27741323, PubMed:28319081, PubMed:28319084). Efficient guide-dependent tDNA cleavage requires a minimal length of 15 bp and is maximal at 19 bp (PubMed:28319081). Prefers gDNA with 5'-phosphorylated purines and 3'-pyrimidines; changing these bases alters the cleavage activity and patterns (PubMed:28319084). Also has guide-independent activity on tDNA called 'chopping' (PubMed:28319081). Probably a first round of guide-independent activity on an invading plasmid or virus would generate guide DNAs for subsequent, more efficient, guide-dependent degradation of invading nucleic acids (PubMed:28319081). Has no activity on substrate with a mismatch at positions 10 and 11, on ssDNA or RNA, nor on DNA:RNA hybrids (PubMed:24442234). Digests longer (750 bp) dsDNA as well as circular plasmid and naked genomic DNA, but not chromatin, in a guide DNA-independent manner (PubMed:28319081). Addition of endogenous histone A3 protects DNA from cleavage, while cleavage is insensitive to methylation (PubMed:28319081). When plasmid encoding active or mutated protein (Ala-541) is transformed into Sulfolobus acidocaldarius about 25-fold fewer transformants are found with active protein; reduced levels of plasmid are found in wild-type transformed cells. While S.acidocaldarius grows at a similar temperature to M.jannaschii (70 to 80 degrees Celsius) it has very different histone-like proteins, which presumably do not protect against MjAgo (PubMed:28319081). Binds ssDNA, dsDNA and DNA-RNA hybrids; binding is most efficient with dsDNA (PubMed:24442234).<ref>PMID:24442234</ref> <ref>PMID:27741323</ref> <ref>PMID:28319081</ref> <ref>PMID:28319084</ref> <ref>PMID:28319081</ref> | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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==See Also== | ==See Also== | ||
*[[Argonaute|Argonaute]] | *[[Argonaute 3D structures|Argonaute 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Methanocaldococcus jannaschii]] | ||
[[Category: | [[Category: Grohmann D]] | ||
[[Category: | [[Category: Keegan R]] | ||
[[Category: | [[Category: Oellig CA]] | ||
[[Category: | [[Category: Schneider S]] | ||
[[Category: | [[Category: Willkomm S]] | ||
[[Category: | [[Category: Zander A]] | ||