3ajv: Difference between revisions

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-[[Image:3ajv.png|left|200px]]
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+==Splicing endonuclease from Aeropyrum pernix==
-The line below this paragraph, containing "STRUCTURE_3ajv", creates the "Structure Box" on the page.
+<StructureSection load='3ajv' size='340' side='right'caption='[[3ajv]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3ajv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix] and [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AJV FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-{{STRUCTURE_3ajv|  PDB=3ajv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ajv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ajv OCA], [https://pdbe.org/3ajv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ajv RCSB], [https://www.ebi.ac.uk/pdbsum/3ajv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ajv ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9YE85_AERPE Q9YE85_AERPE]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In Archaea, splicing endonuclease (EndA) recognizes and cleaves precursor RNAs to remove introns. Currently, EndAs are classified into three families according to their subunit structures: homotetramer, homodimer, and heterotetramer. The crenarchaeal heterotetrameric EndAs can be further classified into two subfamilies based on the size of the structural subunit. Subfamily A possesses a structural subunit similar in size to the catalytic subunit, whereas subfamily B possesses a structural subunit significantly smaller than the catalytic subunit. Previously, we solved the crystal structure of an EndA from Pyrobaculum aerophilum. The endonuclease was classified into subfamily B, and the structure revealed that the enzyme lacks an N-terminal subdomain in the structural subunit. However, no structural information is available for crenarchaeal heterotetrameric EndAs that are predicted to belong to subfamily A. Here, we report the crystal structure of the EndA from Aeropyrum pernix, which is predicted to belong to subfamily A. The enzyme possesses the N-terminal subdomain in the structural subunit, revealing that the two subfamilies of heterotetrameric EndAs are structurally distinct. EndA from A. pernix also possesses an extra loop region that is characteristic of crenarchaeal EndAs. Our mutational study revealed that the conserved lysine residue in the loop is important for endonuclease activity. Furthermore, the sequence characteristics of the loops and the positions towards the substrate RNA according to a docking model prompted us to propose that crenarchaea-specific loops and an extra amino acid sequence at the catalytic loop of nanoarchaeal EndA are derived by independent convergent evolution and function for recognizing noncanonical bulge-helix-bulge motif RNAs as substrates.
-===Splicing endonuclease from Aeropyrum pernix===
+A Conserved Lysine Residue in the Crenarchaea-Specific Loop is Important for the Crenarchaeal Splicing Endonuclease Activity.,Okuda M, Shiba T, Inaoka DK, Kita K, Kurisu G, Mineki S, Harada S, Watanabe YI, Yoshinari S J Mol Biol. 2010 Nov 2. PMID:21050862<ref>PMID:21050862</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ajv" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21050862}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21050862 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21050862}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3ajv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJV OCA].
-==Reference==
-<ref group="xtra">PMID:21050862</ref><references group="xtra"/>
 [[Category: Aeropyrum pernix]]
-[[Category: TRNA-intron endonuclease]]
+[[Category: Aeropyrum pernix K1]]
-[[Category: Inaoka, K D.]]
+[[Category: Large Structures]]
-[[Category: Kurisu, G.]]
+[[Category: Inaoka KD]]
-[[Category: Okuda, M.]]
+[[Category: Kurisu G]]
-[[Category: Shiba, T.]]
+[[Category: Okuda M]]
-[[Category: Watanabe, Y.]]
+[[Category: Shiba T]]
-[[Category: Yoshinari, S.]]
+[[Category: Watanabe Y]]
+[[Category: Yoshinari S]]