1u04

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of full length Argonaute from Pyrococcus furiosus

Structural highlights

1u04 is a 1 chain structure with sequence from Pyrococcus furiosus DSM 3638. The February 2008 RCSB PDB Molecule of the Month feature on Small Interfering RNA by David S. Goodsell is 10.2210/rcsb_pdb/mom_2008_2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AGO_PYRFU A DNA-guided ssDNA endonuclease that may play a role in defense against invading mobile genetic elements. Uses short 5'-phospho-ssDNA sequences as guides (gDNA) to bind complementary target strands, resulting in cleavage of the target DNA (tDNA). Endonucleolytically cleaves DNA in short dsDNA (the gDNA indicates where to cleave on the tDNA). Efficient guide-dependent target DNA cleavage requires a minimal gDNA length of 15 nucleotides (nt) and works up to at least 31 nt. Overexpression decreases plasmid transformation efficiency. Has no appreciable activity with gRNA or on target RNA. Also has guide-independent activity on plasmid DNA called 'chopping' (PubMed:25925567). The cleavage site is 10 nucleotides (nt) downstream of the target residue base-paired with the 5'-end of the gDNA, cleavage is insensitive to adenine methylation. DNA cleavage produces 5'-phosphomonoesters (as it can be ligated by T4 DNA ligase) (PubMed:28165224).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Argonaute proteins and small interfering RNAs (siRNAs) are the known signature components of the RNA interference effector complex RNA-induced silencing complex (RISC). However, the identity of "Slicer," the enzyme that cleaves the messenger RNA (mRNA) as directed by the siRNA, has not been resolved. Here, we report the crystal structure of the Argonaute protein from Pyrococcus furiosus at 2.25 angstrom resolution. The structure reveals a crescent-shaped base made up of the amino-terminal, middle, and PIWI domains. The Piwi Argonaute Zwille (PAZ) domain is held above the base by a "stalk"-like region. The PIWI domain (named for the protein piwi) is similar to ribonuclease H, with a conserved active site aspartate-aspartate-glutamate motif, strongly implicating Argonaute as "Slicer." The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage.

Crystal structure of Argonaute and its implications for RISC slicer activity.,Song JJ, Smith SK, Hannon GJ, Joshua-Tor L Science. 2004 Sep 3;305(5689):1434-7. Epub 2004 Jul 29. PMID:15284453^[3]

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

References

↑ Swarts DC, Hegge JW, Hinojo I, Shiimori M, Ellis MA, Dumrongkulraksa J, Terns RM, Terns MP, van der Oost J. Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Res. 2015 May 26;43(10):5120-9. PMID:25925567 doi:10.1093/nar/gkv415
↑ Enghiad B, Zhao H. Programmable DNA-Guided Artificial Restriction Enzymes. ACS Synth Biol. 2017 May 19;6(5):752-757. PMID:28165224 doi:10.1021/acssynbio.6b00324
↑ Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. Crystal structure of Argonaute and its implications for RISC slicer activity. Science. 2004 Sep 3;305(5689):1434-7. Epub 2004 Jul 29. PMID:15284453 doi:10.1126/science.1102514

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1u04"

@@ Line 3: / Line 3: @@
 <StructureSection load='1u04' size='340' side='right'caption='[[1u04]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1u04]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. The February 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Small Interfering RNA''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_2 10.2210/rcsb_pdb/mom_2008_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U04 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U04 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1u04]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. The February 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Small Interfering RNA''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_2 10.2210/rcsb_pdb/mom_2008_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U04 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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]] 2.25&#8491;</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=1u04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u04 OCA], [http://pdbe.org/1u04 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u04 RCSB], [http://www.ebi.ac.uk/pdbsum/1u04 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u04 ProSAT]</span></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=1u04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u04 OCA], [https://pdbe.org/1u04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u04 RCSB], [https://www.ebi.ac.uk/pdbsum/1u04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u04 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/AGO_PYRFU AGO_PYRFU] A DNA-guided ssDNA endonuclease that may play a role in defense against invading mobile genetic elements. Uses short 5'-phospho-ssDNA sequences as guides (gDNA) to bind complementary target strands, resulting in cleavage of the target DNA (tDNA). Endonucleolytically cleaves DNA in short dsDNA (the gDNA indicates where to cleave on the tDNA). Efficient guide-dependent target DNA cleavage requires a minimal gDNA length of 15 nucleotides (nt) and works up to at least 31 nt. Overexpression decreases plasmid transformation efficiency. Has no appreciable activity with gRNA or on target RNA. Also has guide-independent activity on plasmid DNA called 'chopping' (PubMed:25925567). The cleavage site is 10 nucleotides (nt) downstream of the target residue base-paired with the 5'-end of the gDNA, cleavage is insensitive to adenine methylation. DNA cleavage produces 5'-phosphomonoesters (as it can be ligated by T4 DNA ligase) (PubMed:28165224).<ref>PMID:25925567</ref> <ref>PMID:28165224</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 12: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u0/1u04_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 34: / Line 37: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pyrfu]]
+[[Category: Pyrococcus furiosus DSM 3638]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Small Interfering RNA]]
-[[Category: Hannon, G J]]
+[[Category: Hannon GJ]]
-[[Category: Joshua-Tor, L]]
+[[Category: Joshua-Tor L]]
-[[Category: Smith, S K]]
+[[Category: Smith SK]]
-[[Category: Song, J J]]
+[[Category: Song JJ]]
-[[Category: Argonaute]]
-[[Category: Hydrolase-gene regulation complex]]
-[[Category: Paz]]
-[[Category: Piwi]]
-[[Category: Risc]]
-[[Category: Rnai]]
-[[Category: Rnase h]]
-[[Category: Silencing]]
-[[Category: Slicer]]

1u04

From Proteopedia

Current revision

Crystal structure of full length Argonaute from Pyrococcus furiosus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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