1ipa: Difference between revisions

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-[[Image:1ipa.png|left|200px]]
-{{STRUCTURE_1ipa|  PDB=1ipa  |  SCENE=  }}
+==CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE==
+<StructureSection load='1ipa' size='340' side='right'caption='[[1ipa]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ipa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IPA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IPA FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</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=1ipa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ipa OCA], [https://pdbe.org/1ipa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ipa RCSB], [https://www.ebi.ac.uk/pdbsum/1ipa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ipa ProSAT], [https://www.topsan.org/Proteins/RSGI/1ipa TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7SID4_THETH Q7SID4_THETH]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/1ipa_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1ipa ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 A resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2'-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.
-===CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE===
+An enzyme with a deep trefoil knot for the active-site architecture.,Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1129-37. Epub 2002, Jun 20. PMID:12077432<ref>PMID:12077432</ref>
-{{ABSTRACT_PUBMED_12077432}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1ipa" style="background-color:#fffaf0;"></div>
-[[1ipa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IPA OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:012077432</ref><ref group="xtra">PMID:012486711</ref><references group="xtra"/>
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Chijimatsu, M.]]
+[[Category: Chijimatsu M]]
-[[Category: Hashimoto, K.]]
+[[Category: Hashimoto K]]
-[[Category: Inoue, Y.]]
+[[Category: Inoue Y]]
-[[Category: Ishitani, R.]]
+[[Category: Ishitani R]]
-[[Category: Kuramitsu, S.]]
+[[Category: Kuramitsu S]]
-[[Category: Nureki, O.]]
+[[Category: Nureki O]]
-[[Category: Oshima, T.]]
+[[Category: Oshima T]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Shibata T]]
-[[Category: Shibata, T.]]
+[[Category: Shirouzu M]]
-[[Category: Shirouzu, M.]]
+[[Category: Takio K]]
-[[Category: Takio, K.]]
+[[Category: Tamakoshi M]]
-[[Category: Tamakoshi, M.]]
+[[Category: Terada T]]
-[[Category: Terada, T.]]
+[[Category: Vassylyev DG]]
-[[Category: Vassylyev, D G.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: Deep trefoil knot]]
-[[Category: El30-like fold]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rossmann fold]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]