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| | ==The X-ray crystal structure of subunit fusion RNA splicing endonuclease from Methanopyrus kandleri== | | ==The X-ray crystal structure of subunit fusion RNA splicing endonuclease from Methanopyrus kandleri== |
| - | <StructureSection load='5x89' size='340' side='right' caption='[[5x89]], [[Resolution|resolution]] 1.53Å' scene=''> | + | <StructureSection load='5x89' size='340' side='right'caption='[[5x89]], [[Resolution|resolution]] 1.53Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5x89]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Metka Metka]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X89 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X89 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5x89]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanopyrus_kandleri_AV19 Methanopyrus kandleri AV19]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X89 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.53Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">endA, MK0341 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=190192 METKA])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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_lyase tRNA-intron lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.16 4.6.1.16] </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=5x89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x89 OCA], [https://pdbe.org/5x89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x89 RCSB], [https://www.ebi.ac.uk/pdbsum/5x89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x89 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=5x89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x89 OCA], [http://pdbe.org/5x89 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x89 RCSB], [http://www.ebi.ac.uk/pdbsum/5x89 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x89 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/ENDA_METKA ENDA_METKA] 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.[HAMAP-Rule:MF_01833][https://www.uniprot.org/uniprot/ENDAL_METKA ENDAL_METKA] |
| - | Four different types (alpha4, alpha'2, (alphabeta)2 and epsilon2) of RNA-splicing endonucleases (EndAs) for RNA processing are known to exist in the Archaea. Only the (alphabeta)2 and epsilon2 types can cleave non-canonical introns in precursor (pre)-tRNA. Both enzyme types possess an insert associated with a specific loop, allowing broad substrate specificity in the catalytic alpha units. Here, the hyperthermophilic euryarchaeon Methanopyrus kandleri (MKA) was predicted to harbor an (alphabeta)2-type EndA lacking the specific loop. To characterize MKA EndA enzymatic activity, we constructed a fusion protein derived from MKA alpha and beta subunits (fMKA EndA). In vitro assessment demonstrated complete removal of the canonical bulge-helix-bulge (BHB) intron structure from MKA pre-tRNAAsn. However, removal of the relaxed BHB structure in MKA pre-tRNAGlu was inefficient compared to crenarchaeal (alphabeta)2 EndA, and the ability to process the relaxed intron within mini-helix RNA was not detected. fMKA EndA X-ray structure revealed a shape similar to that of other EndA types, with no specific loop. Mapping of EndA types and their specific loops and the tRNA gene diversity among various Archaea suggest that MKA EndA is evolutionarily related to other (alphabeta)2-type EndAs found in the Thaumarchaeota, Crenarchaeota and Aigarchaeota but uniquely represents constrained substrate specificity.
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| - | The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity.,Kaneta A, Fujishima K, Morikazu W, Hori H, Hirata A Nucleic Acids Res. 2018 Jan 13. pii: 4807343. doi: 10.1093/nar/gky003. PMID:29346615<ref>PMID:29346615</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 5x89" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Metka]] | + | [[Category: Large Structures]] |
| - | [[Category: TRNA-intron lyase]] | + | [[Category: Methanopyrus kandleri AV19]] |
| - | [[Category: Fujishima, K]] | + | [[Category: Fujishima K]] |
| - | [[Category: Hirata, A]] | + | [[Category: Hirata A]] |
| - | [[Category: Hori, H]] | + | [[Category: Hori H]] |
| - | [[Category: Kaneta, A]] | + | [[Category: Kaneta A]] |
| - | [[Category: Morikazu, W]] | + | [[Category: Morikazu W]] |
| - | [[Category: Archaea]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Intron]]
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| - | [[Category: Rna splicing]]
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