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| | <StructureSection load='3p1z' size='340' side='right'caption='[[3p1z]], [[Resolution|resolution]] 2.80Å' scene=''> | | <StructureSection load='3p1z' size='340' side='right'caption='[[3p1z]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3p1z]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P1Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3p1z]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P1Z FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3p1y|3p1y]]</div></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]] 2.8Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE0685 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 AERPX]), endA, APE_1646.1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 AERPX])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/tRNA-intron_endonuclease tRNA-intron endonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.9 3.1.27.9] </span></td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3p1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p1z OCA], [https://pdbe.org/3p1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p1z RCSB], [https://www.ebi.ac.uk/pdbsum/3p1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p1z ProSAT]</span></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=3p1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p1z OCA], [https://pdbe.org/3p1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p1z RCSB], [https://www.ebi.ac.uk/pdbsum/3p1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p1z ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/ENDA_AERPE ENDA_AERPE]] Endonuclease that removes tRNA introns. Cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini. Recognizes a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp (By similarity).
| + | [https://www.uniprot.org/uniprot/Q9YE85_AERPE Q9YE85_AERPE] |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | In Crenarchaea, several tRNA genes are predicted to express precursor-tRNAs (pre-tRNAs) with canonical or non-canonical introns at various positions. We initially focused on the tRNA(Thr) species of hyperthermophilic crenarchaeon, Aeropyrum pernix (APE) and found that in the living APE cells three tRNA(Thr) species were transcribed and subsequently matured to functional tRNAs. During maturation, introns in two of them were cleaved from standard and non-standard positions. Biochemical studies revealed that the APE splicing endonuclease (APE-EndA) removed both types of introns, including the non-canonical introns, without any nucleotide modification. To clarify the underlying reasons for broad substrate specificity of APE-EndA, we determined the crystal structure of wild-type APE-EndA and subsequently compared its structure with that of Archaeaoglobus fulgidus (AFU)-EndA, which has narrow substrate specificity. Remarkably, structural comparison revealed that APE-EndA possesses a Crenarchaea specific loop (CSL). Introduction of CSL into AFU-EndA enhanced its intron-cleaving activity irrespective of the position or motif of the intron. Thus, our biochemical and crystallographic analyses of the chimera-EndA demonstrated that the CSL is responsible for the broad substrate specificity of APE-EndA. Furthermore, mutagenesis studies revealed that Lys44 in CSL functions as the RNA recognition site.
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| - | | + | |
| - | Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop.,Hirata A, Kitajima T, Hori H Nucleic Acids Res. 2011 Nov;39(21):9376-89. Epub 2011 Aug 16. PMID:21846775<ref>PMID:21846775</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
| + | |
| - | <div class="pdbe-citations 3p1z" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aerpx]] | + | [[Category: Aeropyrum pernix]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: TRNA-intron endonuclease]]
| + | [[Category: Hirata A]] |
| - | [[Category: Hirata, A]] | + | |
| - | [[Category: Heterotetramer]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Mixed antiparallel and parallel beta-sheet]]
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| - | [[Category: Rna]]
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| - | [[Category: Rna splicing]]
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| - | [[Category: Splicing endonuclease]]
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