1iyb: Difference between revisions

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-[[Image:1iyb.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1iyb", creates the "Structure Box" on the page.
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-{{STRUCTURE_1iyb|  PDB=1iyb  |  SCENE=  }}
-'''Crystal Structure of the Nicotiana glutinosa Ribonuclease NW'''
+==Crystal Structure of the Nicotiana glutinosa Ribonuclease NW==
+<StructureSection load='1iyb' size='340' side='right'caption='[[1iyb]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1iyb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nicotiana_glutinosa Nicotiana glutinosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IYB 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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</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=1iyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyb OCA], [https://pdbe.org/1iyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iyb RCSB], [https://www.ebi.ac.uk/pdbsum/1iyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iyb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q7XZV5_NICGU Q7XZV5_NICGU]
+== 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/iy/1iyb_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=1iyb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribonuclease NW (RNase NW), the wound-inducible RNase in Nicotiana glutinosa leaves, preferentially cleaves guanylic acid. We expressed the cDNA encoding RNase NW in the methylotrophic yeast Pichia pastoris using the expression vector pPIC9K, and the resulting recombinant RNase NW (ryRNaseNW) secreted into medium was purified to apparent homogeneity using column chromatography. The crystal structure of ryRNase NW bound to 5'-GMP was determined at 1.5 A resolution by molecular replacement with tomato RNase LE as a search model. The RNase NW structurally belongs to the (alpha + beta) class of proteins, having eight helices (five alpha-helices and three 3(10) helices) and six beta-strands, and its structure is highly similar to those of other plant RNases, including a uridylic acid preferential RNase MC1 from bitter gourd seeds. The guanine ring of 5'-GMP lies in a hydrophobic pocket of the molecular surface composed of Tyr17, Tyr71, Ala80, Leu79, and Phe89: the guanine base is sandwiched between aromatic side chains of Tyr17 and Phe89. In addition, the guanine base is firmly stabilized by a network of hydrogen bonds of the side chains of Gln12 and Thr78, as well as of the main chain of Leu79. Therefore, Gln12, Tyr17, Thr78, Leu79, and Phe89 are responsible for recognition of the guanine base by RNase NW, findings which provide insight into the manner in which RNase NW preferentially cleaves guanylic acid.
-==Overview==
+Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallography.,Kawano S, Kakuta Y, Kimura M Biochemistry. 2002 Dec 24;41(51):15195-202. PMID:12484757<ref>PMID:12484757</ref>
-Ribonuclease NW (RNase NW), the wound-inducible RNase in Nicotiana glutinosa leaves, preferentially cleaves guanylic acid. We expressed the cDNA encoding RNase NW in the methylotrophic yeast Pichia pastoris using the expression vector pPIC9K, and the resulting recombinant RNase NW (ryRNaseNW) secreted into medium was purified to apparent homogeneity using column chromatography. The crystal structure of ryRNase NW bound to 5'-GMP was determined at 1.5 A resolution by molecular replacement with tomato RNase LE as a search model. The RNase NW structurally belongs to the (alpha + beta) class of proteins, having eight helices (five alpha-helices and three 3(10) helices) and six beta-strands, and its structure is highly similar to those of other plant RNases, including a uridylic acid preferential RNase MC1 from bitter gourd seeds. The guanine ring of 5'-GMP lies in a hydrophobic pocket of the molecular surface composed of Tyr17, Tyr71, Ala80, Leu79, and Phe89: the guanine base is sandwiched between aromatic side chains of Tyr17 and Phe89. In addition, the guanine base is firmly stabilized by a network of hydrogen bonds of the side chains of Gln12 and Thr78, as well as of the main chain of Leu79. Therefore, Gln12, Tyr17, Thr78, Leu79, and Phe89 are responsible for recognition of the guanine base by RNase NW, findings which provide insight into the manner in which RNase NW preferentially cleaves guanylic acid.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-IYB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Nicotiana_glutinosa Nicotiana glutinosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYB OCA].
+</div>
+<div class="pdbe-citations 1iyb" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Guanine binding site of the Nicotiana glutinosa ribonuclease NW revealed by X-ray crystallography., Kawano S, Kakuta Y, Kimura M, Biochemistry. 2002 Dec 24;41(51):15195-202. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12484757 12484757]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Nicotiana glutinosa]]
-[[Category: Single protein]]
+[[Category: Kakuta Y]]
-[[Category: Kakuta, Y.]]
+[[Category: Kawano S]]
-[[Category: Kawano, S.]]
+[[Category: Kimura M]]
-[[Category: Kimura, M.]]
-[[Category: Hydrolase]]
-[[Category: Ribonuclease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:34:36 2008''