2vmk: Difference between revisions

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-{{Seed}}
-[[Image:2vmk.png|left|200px]]
-<!--
+==Crystal Structure of E. coli RNase E Apoprotein - Catalytic Domain==
-The line below this paragraph, containing "STRUCTURE_2vmk", creates the "Structure Box" on the page.
+<StructureSection load='2vmk' size='340' side='right'caption='[[2vmk]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vmk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VMK FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2vmk|  PDB=2vmk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vmk OCA], [https://pdbe.org/2vmk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vmk RCSB], [https://www.ebi.ac.uk/pdbsum/2vmk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vmk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
+== 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/vm/2vmk_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2vmk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RNase E is an essential bacterial endoribonuclease involved in the turnover of messenger RNA and the maturation of structured RNA precursors in Escherichia coli. Here, we present the crystal structure of the E. coli RNase E catalytic domain in the apo-state at 3.3 A. This structure indicates that, upon catalytic activation, RNase E undergoes a marked conformational change characterized by the coupled movement of two RNA-binding domains to organize the active site. The structural data suggest a mechanism of RNA recognition and cleavage that explains the enzyme's preference for substrates possessing a 5'-monophosphate and accounts for the protective effect of a triphosphate cap for most transcripts. Internal flexibility within the quaternary structure is also observed, a finding that has implications for recognition of structured RNA substrates and for the mechanism of internal entry for a subset of substrates that are cleaved without 5'-end requirements.
-===CRYSTAL STRUCTURE OF E. COLI RNASE E APOPROTEIN- CATALYTIC DOMAIN===
+The crystal structure of the Escherichia coli RNase E apoprotein and a mechanism for RNA degradation.,Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, Scott WG, Luisi BF Structure. 2008 Aug 6;16(8):1238-44. PMID:18682225<ref>PMID:18682225</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vmk" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18682225}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18682225 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18682225}}
+__TOC__
+</StructureSection>
-==About this Structure==
-VMK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VMK OCA].
-==Reference==
-The Crystal Structure of the Escherichia coli RNase E Apoprotein and a Mechanism for RNA Degradation., Koslover DJ, Callaghan AJ, Marcaida MJ, Garman EF, Martick M, Scott WG, Luisi BF, Structure. 2008 Aug;16(8):1238-44. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18682225 18682225]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Callaghan, A J.]]
+[[Category: Callaghan AJ]]
-[[Category: Koslover, D J.]]
+[[Category: Koslover DJ]]
-[[Category: Luisi, B F.]]
+[[Category: Luisi BF]]
-[[Category: Marcaida, M J.]]
+[[Category: Marcaida MJ]]
-[[Category: Martick, M.]]
+[[Category: Martick M]]
-[[Category: Scott, W G.]]
+[[Category: Scott WG]]
-[[Category: Cytoplasm]]
-[[Category: Endonuclease]]
-[[Category: Hydrolase]]
-[[Category: Nuclease]]
-[[Category: Rna processing]]
-[[Category: Rna turnover]]
-[[Category: Rna-binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 20 11:28:16 2008''