1r6l: Difference between revisions

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-[[Image:1r6l.gif|left|200px]]
- {{Structure
+==Crystal Structure Of The tRNA Processing Enzyme Rnase pH From Pseudomonas Aeruginosa==
-|PDB= 1r6l |SIZE=350|CAPTION= <scene name='initialview01'>1r6l</scene>, resolution 1.90&Aring;
+<StructureSection load='1r6l' size='340' side='right'caption='[[1r6l]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <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>
+<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>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_nucleotidyltransferase tRNA nucleotidyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.56 2.7.7.56] </span>
+</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>
-|GENE= RPH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])
+<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>
-|DOMAIN=
+<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>
-|RELATEDENTRY=[[1r6m|1R6M]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r6l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6l OCA], [http://www.ebi.ac.uk/pdbsum/1r6l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1r6l RCSB]</span>
+== 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.
-'''Crystal Structure Of The tRNA Processing Enzyme Rnase pH From Pseudomonas Aeruginosa'''
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1r6l" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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.
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-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].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-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]
 [[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 Sun Mar 30 23:24:00 2008''