1ymn: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:1ymn.gif|left|200px]]
- {{Structure
+==The study of reductive unfolding pathways of RNase A (Y92L mutant)==
-|PDB= 1ymn |SIZE=350|CAPTION= <scene name='initialview01'>1ymn</scene>, resolution 1.45&Aring;
+<StructureSection load='1ymn' size='340' side='right'caption='[[1ymn]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[1ymn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YMN FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
-|GENE= RNASE1, RNS1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 Bos taurus])
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ymn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ymn OCA], [https://pdbe.org/1ymn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ymn RCSB], [https://www.ebi.ac.uk/pdbsum/1ymn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ymn ProSAT]</span></td></tr>
-}}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNAS1_BOVIN RNAS1_BOVIN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:7479688</ref>
+== 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/ym/1ymn_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=1ymn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Reductive unfolding studies of proteins are designed to provide information about intramolecular interactions that govern the formation (and stabilization) of the native state and about folding/unfolding pathways. By mutating Tyr92 to G, A, or L in the model protein, bovine pancreatic ribonuclease A, and through analysis of temperature factors and molecular dynamics simulations of the crystal structures of these mutants, it is demonstrated that the markedly different reductive unfolding rates and pathways of ribonuclease A and its structural homologue onconase can be attributed to a single, localized, ring-stacking interaction between Tyr92 and Pro93 in the bovine variant. The fortuitous location of this specific stabilizing interaction in a disulfide-bond-containing loop region of ribonuclease A results in the localized modulation of protein dynamics that, in turn, enhances the susceptibility of the disulfide bond to reduction leading to an alteration in the reductive unfolding behavior of the homologues. These results have important implications for folding studies involving topological determinants to obtain folding/unfolding rates and pathways, for protein structure-function prediction through fold recognition, and for predicting proteolytic cleavage sites.
-'''The study of reductive unfolding pathways of RNase A (Y92L mutant)'''
+A localized specific interaction alters the unfolding pathways of structural homologues.,Xu G, Narayan M, Kurinov I, Ripoll DR, Welker E, Khalili M, Ealick SE, Scheraga HA J Am Chem Soc. 2006 Feb 1;128(4):1204-13. PMID:16433537<ref>PMID:16433537</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ymn" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Reductive unfolding studies of proteins are designed to provide information about intramolecular interactions that govern the formation (and stabilization) of the native state and about folding/unfolding pathways. By mutating Tyr92 to G, A, or L in the model protein, bovine pancreatic ribonuclease A, and through analysis of temperature factors and molecular dynamics simulations of the crystal structures of these mutants, it is demonstrated that the markedly different reductive unfolding rates and pathways of ribonuclease A and its structural homologue onconase can be attributed to a single, localized, ring-stacking interaction between Tyr92 and Pro93 in the bovine variant. The fortuitous location of this specific stabilizing interaction in a disulfide-bond-containing loop region of ribonuclease A results in the localized modulation of protein dynamics that, in turn, enhances the susceptibility of the disulfide bond to reduction leading to an alteration in the reductive unfolding behavior of the homologues. These results have important implications for folding studies involving topological determinants to obtain folding/unfolding rates and pathways, for protein structure-function prediction through fold recognition, and for predicting proteolytic cleavage sites.
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-YMN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YMN OCA].
+__TOC__
+</StructureSection>
-==Reference==
-A localized specific interaction alters the unfolding pathways of structural homologues., Xu G, Narayan M, Kurinov I, Ripoll DR, Welker E, Khalili M, Ealick SE, Scheraga HA, J Am Chem Soc. 2006 Feb 1;128(4):1204-13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16433537 16433537]
 [[Category: Bos taurus]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Ealick SE]]
-[[Category: Ealick, S E.]]
+[[Category: Khalili M]]
-[[Category: Khalili, M.]]
+[[Category: Kurinov I]]
-[[Category: Kurinov, I.]]
+[[Category: Narayan M]]
-[[Category: Narayan, M.]]
+[[Category: Ripoll DR]]
-[[Category: Ripoll, D R.]]
+[[Category: Scheraga HA]]
-[[Category: Scheraga, H A.]]
+[[Category: Welker E]]
-[[Category: Welker, E.]]
+[[Category: Xu G]]
-[[Category: Xu, G.]]
-[[Category: hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:24:49 2008''