1rds: Difference between revisions

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-[[Image:1rds.gif|left|200px]]<br /><applet load="1rds" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1rds, resolution 1.8&Aring;" />
-'''CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE==
-A ribonuclease T1 homologue, ribonuclease Ms (RNase Ms) from Aspergillus, saitoi, has been crystallized as a complex with a substrate analogue GfpC, where the 2'-hydroxyl (2'-OH) group of guanosine in, guanylyl-3',5'-cytidine (GpC) is replaced by the 2'-fluorine (2'-F) atom, to prevent transesterification. The crystal structure of the complex was, solved at 1.8-A resolution to a final R-factor of 0.204. The role of His92, (RNase T1 numbering) as the general acid catalyst was confirmed. Of the, two alternative candidates for a general base to abstract a proton from, the 2'-OH group, His40 and Glu58 were found close to the 2'-F atom, making, the decision between the two groups difficult. We then superposed the, active site of the RNase Ms/GfpC complex with that of pancreatic, ribonuclease S (RNase S) complexed with a substrate analogue UpcA, a, phosphonate analogue of uridylyl-3',5'-adenosine (UpA), and found that, His12 and His119 of RNase A almost exactly coincided with Glu58 and His92, respectively, of RNase Ms. Similar superposition with a prokaryotic, microbial ribonuclease, RNase St [Nakamura, K. T., Iwahashi, K., Yamamoto, Y., Iitaka, Y., Yoshida, N., &amp; Mitsui, Y. (1982) Nature 299, 564-566], also indicated Glu58 as a general base. Thus the present comparative, geometrical studies consistently favor, albeit indirectly, the traditional, as well as the most recent notion [Steyaert, J., Hallenga, K., Wyns, L., &amp;, Stanssens, P. (1990) Biochemistry 29, 9064-9072] that Glu58, rather than, His40, must be the general base catalyst in the intact enzymes of the, RNase T1 family.
+<StructureSection load='1rds' size='340' side='right'caption='[[1rds]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1rds]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_phoenicis Aspergillus phoenicis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RDS 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]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GPC:2-FLUOROGUANYLYL-(3-5)-PHOSPHOCYTIDINE'>GPC</scene></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=1rds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rds OCA], [https://pdbe.org/1rds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rds RCSB], [https://www.ebi.ac.uk/pdbsum/1rds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rds ProSAT]</span></td></tr>
+</table>
+== 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/rd/1rds_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=1rds ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A ribonuclease T1 homologue, ribonuclease Ms (RNase Ms) from Aspergillus saitoi, has been crystallized as a complex with a substrate analogue GfpC where the 2'-hydroxyl (2'-OH) group of guanosine in guanylyl-3',5'-cytidine (GpC) is replaced by the 2'-fluorine (2'-F) atom to prevent transesterification. The crystal structure of the complex was solved at 1.8-A resolution to a final R-factor of 0.204. The role of His92 (RNase T1 numbering) as the general acid catalyst was confirmed. Of the two alternative candidates for a general base to abstract a proton from the 2'-OH group, His40 and Glu58 were found close to the 2'-F atom, making the decision between the two groups difficult. We then superposed the active site of the RNase Ms/GfpC complex with that of pancreatic ribonuclease S (RNase S) complexed with a substrate analogue UpcA, a phosphonate analogue of uridylyl-3',5'-adenosine (UpA), and found that His12 and His119 of RNase A almost exactly coincided with Glu58 and His92, respectively, of RNase Ms. Similar superposition with a prokaryotic microbial ribonuclease, RNase St [Nakamura, K. T., Iwahashi, K., Yamamoto, Y., Iitaka, Y., Yoshida, N., &amp; Mitsui, Y. (1982) Nature 299, 564-566], also indicated Glu58 as a general base. Thus the present comparative geometrical studies consistently favor, albeit indirectly, the traditional as well as the most recent notion [Steyaert, J., Hallenga, K., Wyns, L., &amp; Stanssens, P. (1990) Biochemistry 29, 9064-9072] that Glu58, rather than His40, must be the general base catalyst in the intact enzymes of the RNase T1 family.
-==About this Structure==
+Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue.,Nonaka T, Nakamura KT, Uesugi S, Ikehara M, Irie M, Mitsui Y Biochemistry. 1993 Nov 9;32(44):11825-37. PMID:8218254<ref>PMID:8218254</ref>
-RDS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_phoenicis Aspergillus phoenicis] with GPC as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_T(1) Ribonuclease T(1)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.3 3.1.27.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RDS OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue., Nonaka T, Nakamura KT, Uesugi S, Ikehara M, Irie M, Mitsui Y, Biochemistry. 1993 Nov 9;32(44):11825-37. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8218254 8218254]
+</div>
+<div class="pdbe-citations 1rds" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Aspergillus phoenicis]]
-[[Category: Ribonuclease T(1)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Mitsui Y]]
-[[Category: Mitsui, Y.]]
+[[Category: Nakamura KT]]
-[[Category: Nakamura, K.T.]]
+[[Category: Nonaka T]]
-[[Category: Nonaka, T.]]
-[[Category: GPC]]
-[[Category: hydrolase(endoribonuclease)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:30:19 2007''