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| | ==Splicing endonuclease from Aeropyrum pernix== | | ==Splicing endonuclease from Aeropyrum pernix== |
| - | <StructureSection load='3ajv' size='340' side='right' caption='[[3ajv]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='3ajv' size='340' side='right'caption='[[3ajv]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ajv]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe] and [http://en.wikipedia.org/wiki/Aerpx Aerpx]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AJV FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.7Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">APE0685, APE1646, APE_0685 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE]), endA, APE_1646.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=56636 AERPX])</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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA-intron_endonuclease tRNA-intron endonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.9 3.1.27.9] </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=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> |
| - | <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=3ajv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ajv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ajv RCSB], [http://www.ebi.ac.uk/pdbsum/3ajv PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3ajv" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Endonuclease|Endonuclease]] | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aerpe]] | + | [[Category: Aeropyrum pernix]] |
| - | [[Category: Aerpx]] | + | [[Category: Aeropyrum pernix K1]] |
| - | [[Category: TRNA-intron endonuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Inaoka, K D]] | + | [[Category: Inaoka KD]] |
| - | [[Category: Kurisu, G]] | + | [[Category: Kurisu G]] |
| - | [[Category: Okuda, M]] | + | [[Category: Okuda M]] |
| - | [[Category: Shiba, T]] | + | [[Category: Shiba T]] |
| - | [[Category: Watanabe, Y]] | + | [[Category: Watanabe Y]] |
| - | [[Category: Yoshinari, S]] | + | [[Category: Yoshinari S]] |
| - | [[Category: Archaea crenarchaea]]
| + | |
| - | [[Category: Enda]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Splicing endonuclease]]
| + | |
| - | [[Category: Trna splicing]]
| + | |
| Structural highlights
Function
Q9YE85_AERPE
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Okuda M, Shiba T, Inaoka DK, Kita K, Kurisu G, Mineki S, Harada S, Watanabe YI, Yoshinari S. A Conserved Lysine Residue in the Crenarchaea-Specific Loop is Important for the Crenarchaeal Splicing Endonuclease Activity. J Mol Biol. 2010 Nov 2. PMID:21050862 doi:10.1016/j.jmb.2010.10.050
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