1r6l: Difference between revisions

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-[[Image:1r6l.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1r6l", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
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-{{STRUCTURE_1r6l|  PDB=1r6l  |  SCENE=  }}
-'''Crystal Structure Of The tRNA Processing Enzyme Rnase pH From Pseudomonas Aeruginosa'''
+==Crystal Structure Of The tRNA Processing Enzyme Rnase pH From Pseudomonas Aeruginosa==
+<StructureSection load='1r6l' size='340' side='right'caption='[[1r6l]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1r6l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R6L 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1r6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6l OCA], [https://pdbe.org/1r6l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r6l RCSB], [https://www.ebi.ac.uk/pdbsum/1r6l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r6l ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNPH_PSEAE RNPH_PSEAE] Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates (By similarity).
+== 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/r6/1r6l_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=1r6l ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RNase PH is a phosphate-dependent exoribonuclease that catalyzes the removal of nucleotides at the 3' end of the tRNA precursor, leading to the release of nucleoside diphosphate, and generates the CCA end during the maturation process. The 1.9-A crystal structures of the apo and the phosphate-bound forms of RNase PH from Pseudomonas aeruginosa reveal a monomeric RNase PH with an alpha/beta-fold tightly associated into a hexameric ring structure in the form of a trimer of dimers. A five ion pair network, Glu-63-Arg-74-Asp-116-Arg-77-Asp-118 and an ion-pair Glu-26-Arg-69 that are positioned symmetrically in the trimerization interface play critical roles in the formation of a hexameric ring. Single or double mutations of Arg-69, Arg-74, or Arg-77 in these ion pairs leads to the dissociation of the RNase PH hexamer into dimers without perturbing the overall monomeric structure. The dissociated RNase PH dimer completely lost its binding affinity and catalytic activity against a precursor tRNA. Our structural and mutational analyses of RNase PH demonstrate that the hexameric ring formation is a critical feature for the function of members of the RNase PH family.
-==Overview==
+Probing the functional importance of the hexameric ring structure of RNase PH.,Choi JM, Park EY, Kim JH, Chang SK, Cho Y J Biol Chem. 2004 Jan 2;279(1):755-64. Epub 2003 Oct 22. PMID:14573594<ref>PMID:14573594</ref>
-RNase PH is a phosphate-dependent exoribonuclease that catalyzes the removal of nucleotides at the 3' end of the tRNA precursor, leading to the release of nucleoside diphosphate, and generates the CCA end during the maturation process. The 1.9-A crystal structures of the apo and the phosphate-bound forms of RNase PH from Pseudomonas aeruginosa reveal a monomeric RNase PH with an alpha/beta-fold tightly associated into a hexameric ring structure in the form of a trimer of dimers. A five ion pair network, Glu-63-Arg-74-Asp-116-Arg-77-Asp-118 and an ion-pair Glu-26-Arg-69 that are positioned symmetrically in the trimerization interface play critical roles in the formation of a hexameric ring. Single or double mutations of Arg-69, Arg-74, or Arg-77 in these ion pairs leads to the dissociation of the RNase PH hexamer into dimers without perturbing the overall monomeric structure. The dissociated RNase PH dimer completely lost its binding affinity and catalytic activity against a precursor tRNA. Our structural and mutational analyses of RNase PH demonstrate that the hexameric ring formation is a critical feature for the function of members of the RNase PH family.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-R6L is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R6L OCA].
+</div>
+<div class="pdbe-citations 1r6l" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Probing the functional importance of the hexameric ring structure of RNase PH., Choi JM, Park EY, Kim JH, Chang SK, Cho Y, J Biol Chem. 2004 Jan 2;279(1):755-64. Epub 2003 Oct 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14573594 14573594]
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Single protein]]
+[[Category: Chang SK]]
-[[Category: TRNA nucleotidyltransferase]]
+[[Category: Cho Y]]
-[[Category: Chang, S K.]]
+[[Category: Choi JM]]
-[[Category: Cho, Y.]]
+[[Category: Kim JH]]
-[[Category: Choi, J M.]]
+[[Category: Park EY]]
-[[Category: Kim, J H.]]
-[[Category: Park, E Y.]]
-[[Category: Beta-alpha-beta-alpha fold]]
-[[Category: Hexamer]]
-[[Category: Phosphate bound]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:08:44 2008''