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| | <StructureSection load='3iey' size='340' side='right'caption='[[3iey]], [[Resolution|resolution]] 2.11Å' scene=''> | | <StructureSection load='3iey' size='340' side='right'caption='[[3iey]], [[Resolution|resolution]] 2.11Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3iey]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"nanoarchaeum_equitans"_huber_et_al._2002 "nanoarchaeum equitans" huber et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3iey]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nanoarchaeum_equitans Nanoarchaeum equitans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IEY 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;'>[[3if0|3if0]]</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]] 2.11Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">endA, NEQ205 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160232 "Nanoarchaeum equitans" Huber et al. 2002]), NEQ261 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=160232 "Nanoarchaeum equitans" Huber et al. 2002])</td></tr>
| + | |
| - | <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>
| + | |
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3iey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iey OCA], [https://pdbe.org/3iey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iey RCSB], [https://www.ebi.ac.uk/pdbsum/3iey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iey 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=3iey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iey OCA], [https://pdbe.org/3iey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iey RCSB], [https://www.ebi.ac.uk/pdbsum/3iey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iey ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/ENDA_NANEQ ENDA_NANEQ]] 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/ENDA_NANEQ ENDA_NANEQ] 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). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </div> | | </div> |
| | <div class="pdbe-citations 3iey" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 3iey" style="background-color:#fffaf0;"></div> |
| - | | |
| - | ==See Also== | |
| - | *[[Endonuclease 3D structures|Endonuclease 3D structures]] | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Nanoarchaeum equitans huber et al. 2002]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: TRNA-intron endonuclease]] | + | [[Category: Nanoarchaeum equitans]] |
| - | [[Category: Li, H]] | + | [[Category: Li H]] |
| - | [[Category: Mitchell, M]] | + | [[Category: Mitchell M]] |
| - | [[Category: Endonuclease]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolase-rna binding protein complex]]
| + | |
| - | [[Category: Nuclease]]
| + | |
| - | [[Category: Protein heterodimer]]
| + | |
| - | [[Category: Trna processing]]
| + | |
| Structural highlights
Function
ENDA_NANEQ 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).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The RNA splicing and processing endonuclease from Nanoarchaeum equitans (NEQ) belongs to the recently identified (alphabeta)(2) family of splicing endonucleases that require two different subunits for splicing activity. N. equitans splicing endonuclease comprises the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Here, we report the crystal structure of the functional NEQ enzyme at 2.1 A containing both subunits, as well as that of the NEQ261 subunit alone at 2.2 A. The functional enzyme resembles previously known alpha(2) and alpha(4) endonucleases but forms a heterotetramer: a dimer of two heterodimers of the catalytic subunit (NEQ205) and the structural subunit (NEQ261). Surprisingly, NEQ261 alone forms a homodimer, similar to the previously known homodimer of the catalytic subunit. The homodimers of isolated subunits are inhibitory to heterodimerization as illustrated by a covalently linked catalytic homodimer that had no RNA cleavage activity upon mixing with the structural subunit. Detailed structural comparison reveals a more favorable hetero- than homodimerization interface, thereby suggesting a possible regulation mechanism of enzyme assembly through available subunits. Finally, the uniquely flexible active site of the NEQ endonuclease provides a possible explanation for its broader substrate specificity.
Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease.,Mitchell M, Xue S, Erdman R, Randau L, Soll D, Li H Nucleic Acids Res. 2009 Sep;37(17):5793-802. Epub 2009 Jul 3. PMID:19578064[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Mitchell M, Xue S, Erdman R, Randau L, Soll D, Li H. Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease. Nucleic Acids Res. 2009 Sep;37(17):5793-802. Epub 2009 Jul 3. PMID:19578064 doi:10.1093/nar/gkp537
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