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==Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21 space group==
==Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21 space group==
<StructureSection load='1r11' size='340' side='right' caption='[[1r11]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
<StructureSection load='1r11' size='340' side='right'caption='[[1r11]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1r11]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R11 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1r11]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R11 FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1r0v|1r0v]]</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]] 2.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ENDA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</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=1r11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r11 OCA], [https://pdbe.org/1r11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r11 RCSB], [https://www.ebi.ac.uk/pdbsum/1r11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r11 ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r11 OCA], [http://pdbe.org/1r11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r11 RCSB], [http://www.ebi.ac.uk/pdbsum/1r11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1r11 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/ENDA_ARCFU ENDA_ARCFU]] 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.  
[https://www.uniprot.org/uniprot/ENDA_ARCFU ENDA_ARCFU] 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.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1r11 ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1r11 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
RNA-splicing endonuclease is responsible for the excision of introns in transfer RNA and archaeal ribosomal RNAs. The archaeal form of the enzyme recognizes a unique RNA motif that consists of two three-nucleotide bulges separated by a four base-paired helix, known as the bulge-helix-bulge (BHB) motif. A crystal structure of the RNA-splicing endonuclease from Archaeoglobus fulgidus (AF) has been reported previously at 2.8 A. A truncated but fully active form of AF endonuclease that lacks the N-terminal domain was expressed and crystallized in an orthorhombic space group with two dimers in the asymmetric unit. The calculated native Patterson map suggests strong pseudo-face-centering characteristics, which lead to incorrect space-group assignment by the autoindexing program. The correct space group was determined to be P2(1)2(1)2 after reindexing. The structure was solved using molecular replacement and was refined to 2.0 A. The truncated AF endonuclease structure is essentially identical to the corresponding portion of the wild-type AF endonuclease structure in space group P4(3)2(1)2 as reported previously, with the exception of loop L9, which differs owing to different crystallographic packing. These results confirm the previously described structural features of dimeric splicing endonuclease.
Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2.,Zhang Y, Li H Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):447-52. Epub 2004, Feb 25. PMID:14993668<ref>PMID:14993668</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1r11" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Arcfu]]
[[Category: Archaeoglobus fulgidus DSM 4304]]
[[Category: TRNA-intron endonuclease]]
[[Category: Large Structures]]
[[Category: Li, H]]
[[Category: Li H]]
[[Category: Zhang, Y]]
[[Category: Zhang Y]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Rna splicing]]
[[Category: Translation]]
[[Category: X-ray crystallography]]

Latest revision as of 08:19, 14 February 2024

Structure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21 space group

1r11, resolution 2.70Å

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