3d5g: Difference between revisions

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-{{Seed}}
-[[Image:3d5g.png|left|200px]]
-<!--
+==Structure of ribonuclease Sa2 complexes with mononucleotides: new aspects of catalytic reaction and substrate recognition==
-The line below this paragraph, containing "STRUCTURE_3d5g", creates the "Structure Box" on the page.
+<StructureSection load='3d5g' size='340' side='right'caption='[[3d5g]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3d5g]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Kitasatospora_aureofaciens Kitasatospora aureofaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D5G FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3d5g|  PDB=3d5g  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d5g OCA], [https://pdbe.org/3d5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d5g RCSB], [https://www.ebi.ac.uk/pdbsum/3d5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d5g ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q53752_KITAU Q53752_KITAU]
+== 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/d5/3d5g_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3d5g ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Although the mechanism of RNA cleavage by RNases has been studied for many years, there remain aspects that have not yet been fully clarified. We have solved the crystal structures of RNase Sa2 in the apo form and in complexes with mononucleotides. These structures provide more details about the mechanism of RNA cleavage by RNase Sa2. In addition to Glu56 and His86, which are the principal catalytic residues, an important role in the first reaction step of RNA cleavage also seems to be played by Arg67 and Arg71, which are located in the phosphate-binding site and form hydrogen bonds with the oxygens of the phosphate group of the mononucleotides. Their positive charge very likely causes polarization of the bonds between the oxygens and the phosphorus atom, leading to electron deficiency on the phosphorus atom and facilitating nucleophilic attack by O2' of the ribose on the phosphorus atom, leading to cyclophosphate formation. The negatively charged Glu56 is in position to attract the proton from O2' of the ribose. Extended molecular docking of mononucleotides, dinucleotides and trinucleotides into the active site of the enzyme allowed us to better understand the guanosine specificity of RNase Sa2 and to predict possible binding subsites for the downstream base and ribose of the second and third nucleotides.
-===Structure of ribonuclease Sa2 complexes with mononucleotides: new aspects of catalytic reaction and substrate recognition===
+Structure of RNase Sa2 complexes with mononucleotides--new aspects of catalytic reaction and substrate recognition.,Bauerova-Hlinkova V, Dvorsky R, Perecko D, Povazanec F, Sevcik J FEBS J. 2009 Aug;276(15):4156-68. Epub 2009 Jun 25. PMID:19558492<ref>PMID:19558492</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3d5g" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19558492}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19558492 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19558492}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Kitasatospora aureofaciens]]
-D5G is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptomyces_aureofaciens Streptomyces aureofaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D5G OCA].
+[[Category: Large Structures]]
+[[Category: Bauerova-Hlinkova V]]
-==Reference==
+[[Category: Dvorsky R]]
-<ref group="xtra">PMID:19558492</ref><references group="xtra"/>
+[[Category: Povazanec F]]
-[[Category: Streptomyces aureofaciens]]
+[[Category: Sevcik J]]
-[[Category: Bauerova-Hlinkova, V.]]
-[[Category: Dvorsky, R.]]
-[[Category: Povazanec, F.]]
-[[Category: Sevcik, J.]]
-[[Category: Hydrolase]]
-[[Category: Ribonuclease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug  5 09:09:58 2009''