1obs: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1obs.gif|left|200px]]<br /><applet load="1obs" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1obs, resolution 2.2&Aring;" />
-'''STRUCTURE OF RICIN A CHAIN MUTANT'''<br />
-==Overview==
+==STRUCTURE OF RICIN A CHAIN MUTANT==
-The A chain of ricin (RTA) is an N-glycosidase which inactivates ribosomes, by removing a single adenine base from a conserved region of rRNA. X-ray, structures and site-directed mutagenesis revealed that Arg 180 interacts, with the target adenine hydrogen bonding with N3. It may fully or, partially protonate that atom as part of the hydrolysis mechanism. Arg 180, was previously converted to His (R180H) and shown to greatly reduce, activity. Here R180H is shown to reduce overall activity 500-fold against, Artemia salina ribosomes. A 2.2 A crystal structure reveals the mutation, causes a rearrangement of the active site cleft, with Tyr 80 moving to, block access to the adenine recognition site. His 180 forms a strong, aromatic interaction with Trp 211, Tyr 80, and Tyr 123. A complex is, formed with 250 mM AMP. The nucleotide binds in the active site region, but in an apparently nonproductive orientation. His 180 cannot bond to N3, and is screened from the substrate analog by the intervening Tyr 80. It, may be that natural polynucleotide substrates, using additional, interactions, can displace Tyr 80 and effect a productive binding.
+<StructureSection load='1obs' size='340' side='right'caption='[[1obs]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1obs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OBS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OBS 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]] 2.2&#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=1obs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1obs OCA], [https://pdbe.org/1obs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1obs RCSB], [https://www.ebi.ac.uk/pdbsum/1obs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1obs ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RICI_RICCO RICI_RICCO] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).
+== 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/ob/1obs_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=1obs ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-OBS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Active as [http://en.wikipedia.org/wiki/rRNA_N-glycosylase rRNA N-glycosylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.22 3.2.2.22] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OBS OCA].
+*[[Ricin 3D structures|Ricin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Structure and activity of an active site substitution of ricin A chain., Day PJ, Ernst SR, Frankel AE, Monzingo AF, Pascal JM, Molina-Svinth MC, Robertus JD, Biochemistry. 1996 Aug 27;35(34):11098-103. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8780513 8780513]
+[[Category: Large Structures]]
 [[Category: Ricinus communis]]
-[[Category: Single protein]]
+[[Category: Day PJ]]
-[[Category: rRNA N-glycosylase]]
+[[Category: Ernst SR]]
-[[Category: Day, P.J.]]
+[[Category: Frankel AE]]
-[[Category: Ernst, S.R.]]
+[[Category: Monzingo AF]]
-[[Category: Frankel, A.E.]]
+[[Category: Pascal JM]]
-[[Category: Monzingo, A.F.]]
+[[Category: Robertus JD]]
-[[Category: Pascal, J.M.]]
+[[Category: Svinth M]]
-[[Category: Robertus, J.D.]]
-[[Category: Svinth, M.]]
-[[Category: duplication]]
-[[Category: glycoprotein]]
-[[Category: glycosidase]]
-[[Category: hydrolase]]
-[[Category: lectin]]
-[[Category: repeat]]
-[[Category: signal]]
-[[Category: toxin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:54:08 2007''