4h4a: Difference between revisions

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-[[Image:4h4a.png|left|200px]]
-{{STRUCTURE_4h4a|  PDB=4h4a  |  SCENE=  }}
+==Crystal structure of the C-terminal domain of Drosophila melanogaster Zucchini==
+<StructureSection load='4h4a' size='340' side='right'caption='[[4h4a]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4h4a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H4A FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</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=4h4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4a OCA], [https://pdbe.org/4h4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h4a RCSB], [https://www.ebi.ac.uk/pdbsum/4h4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h4a ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ZUC_DROME ZUC_DROME] Cardiolipin hydrolase present at the mitochondrial outer membrane required for piRNA metabolic process. Acts by catalyzing the hydrolysis of cardiolipin (diphosphatidylglycerol) to form phosphatidate (phosphatidic acid or PA) at the mitochondrial outer membrane surface, promoting the piRNA metabolic process. Plays a key role in primary biogenesis of piRNAs and is required during oogenesis to repress transposable elements and prevent their mobilization. piRNAs mediate the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Involved in trans-silencing effect (TSE), a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin via its role in piRNA biogenesis.<ref>PMID:17543859</ref> <ref>PMID:19812547</ref> <ref>PMID:20818334</ref> <ref>PMID:20966047</ref> <ref>PMID:20966049</ref> <ref>PMID:20559422</ref> <ref>PMID:21397848</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Piwi-interacting RNAs (piRNAs) are a gonad-specific class of small RNAs that associate with the Piwi clade of Argonaute proteins and play a key role in transposon silencing in animals. Since biogenesis of piRNAs is independent of the double-stranded RNA-processing enzyme Dicer, an alternative nuclease that can process single-stranded RNA transcripts has been long sought. A Phospholipase D-like protein, Zucchini, that is essential for piRNA processing has been proposed to be a nuclease acting in piRNA biogenesis. Here we describe the crystal structure of Zucchini from Drosophila melanogaster and show that it is very similar to the bacterial endonuclease, Nuc. The structure also reveals that homodimerization induces major conformational changes assembling the active site. The active site is situated on the dimer interface at the bottom of a narrow groove that can likely accommodate single-stranded nucleic acid substrates. Furthermore, biophysical analysis identifies protein segments essential for dimerization and provides insights into regulation of Zucchini's activity.
-===Crystal structure of the C-terminal domain of Drosophila melanogaster Zucchini===
+Crystal structure of the primary piRNA biogenesis factor Zucchini reveals similarity to the bacterial PLD endonuclease Nuc.,Voigt F, Reuter M, Kasaruho A, Schulz EC, Pillai RS, Barabas O RNA. 2012 Oct 19. PMID:23086923<ref>PMID:23086923</ref>
-{{ABSTRACT_PUBMED_23086923}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 4h4a" style="background-color:#fffaf0;"></div>
-[[4h4a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4A OCA].
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Drosophila melanogaster]]
-[[Category: Barabas, O.]]
+[[Category: Large Structures]]
-[[Category: Schulz, E C.]]
+[[Category: Barabas O]]
-[[Category: Voigt, F.]]
+[[Category: Schulz EC]]
-[[Category: Hkd motif]]
+[[Category: Voigt F]]
-[[Category: Hydrolase]]
-[[Category: Nuclease/phospholipid hydrolase]]
-[[Category: Nucleic acid/phospholipid]]
-[[Category: Phospholipase d fold]]