|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of the fourth type of archaeal tRNA splicing endonuclease from Candidatus Micrarchaeum acidiphilum ARMAN-2== | | ==Crystal structure of the fourth type of archaeal tRNA splicing endonuclease from Candidatus Micrarchaeum acidiphilum ARMAN-2== |
| - | <StructureSection load='4fz2' size='340' side='right' caption='[[4fz2]], [[Resolution|resolution]] 2.25Å' scene=''> | + | <StructureSection load='4fz2' size='340' side='right'caption='[[4fz2]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fz2]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_micrarchaeum_acidiphilum_arman-2 Candidatus micrarchaeum acidiphilum arman-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FZ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FZ2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fz2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Micrarchaeum_acidiphilum_ARMAN-2 Candidatus Micrarchaeum acidiphilum ARMAN-2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FZ2 FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UNLARM2_0797 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=425595 Candidatus Micrarchaeum acidiphilum ARMAN-2])</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]] 2.252Å</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=4fz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fz2 OCA], [https://pdbe.org/4fz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fz2 RCSB], [https://www.ebi.ac.uk/pdbsum/4fz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fz2 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=4fz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fz2 OCA], [http://pdbe.org/4fz2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fz2 RCSB], [http://www.ebi.ac.uk/pdbsum/4fz2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fz2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/C7DIA5_MICA2 C7DIA5_MICA2] |
| - | Cleavage of introns from precursor transfer RNAs (tRNAs) by tRNA splicing endonuclease (EndA) is essential for tRNA maturation in Archaea and Eukarya. In the past, archaeal EndAs were classified into three types (alpha'2, alpha4 and alpha2beta2) according to subunit composition. Recently, we have identified a fourth type of archaeal EndA from an uncultivated archaeon Candidatus Micrarchaeum acidiphilum, referred to as ARMAN-2, which is deeply branched within Euryarchaea. The ARMAN-2 EndA forms an epsilon2 homodimer and has broad substrate specificity like the alpha2beta2 type EndAs found in Crenarchaea and Nanoarchaea. However, the precise architecture of ARMAN-2 EndA was unknown. Here, we report the crystal structure of the epsilon2 homodimer of ARMAN-2 EndA. The structure reveals that the epsilon protomer is separated into three novel units (alphaN, alpha and betaC) fused by two distinct linkers, although the overall structure of ARMAN-2 EndA is similar to those of the other three types of archaeal EndAs. Structural comparison and mutational analyses reveal that an ARMAN-2 type-specific loop (ASL) is involved in the broad substrate specificity and that K161 in the ASL functions as the RNA recognition site. These findings suggest that the broad substrate specificities of epsilon2 and alpha2beta2 EndAs were separately acquired through different evolutionary processes.
| + | |
| - | | + | |
| - | X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity.,Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H Nucleic Acids Res. 2012 Nov 1;40(20):10554-66. doi: 10.1093/nar/gks826. Epub 2012, Aug 31. PMID:22941657<ref>PMID:22941657</ref>
| + | |
| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 4fz2" style="background-color:#fffaf0;"></div>
| + | |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Endonuclease|Endonuclease]] | + | *[[Endonuclease 3D structures|Endonuclease 3D structures]] |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Candidatus micrarchaeum acidiphilum arman-2]] | + | [[Category: Candidatus Micrarchaeum acidiphilum ARMAN-2]] |
| - | [[Category: TRNA-intron endonuclease]] | + | [[Category: Large Structures]] |
| - | [[Category: Banfiled, J F]] | + | [[Category: Banfiled JF]] |
| - | [[Category: Fujishima, K]] | + | [[Category: Fujishima K]] |
| - | [[Category: Hirata, A]] | + | [[Category: Hirata A]] |
| - | [[Category: Hori, H]] | + | [[Category: Hori H]] |
| - | [[Category: Kanai, A]] | + | [[Category: Kanai A]] |
| - | [[Category: Kawamura, T]] | + | [[Category: Kawamura T]] |
| - | [[Category: Yamagami, R]] | + | [[Category: Yamagami R]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Trna splicing endonuclease]]
| + | |
