2bx2: 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: @@
-{{Seed}}
-[[Image:2bx2.png|left|200px]]
-<!--
+==Catalytic domain of E. coli RNase E==
-The line below this paragraph, containing "STRUCTURE_2bx2", creates the "Structure Box" on the page.
+<StructureSection load='2bx2' size='340' side='right'caption='[[2bx2]], [[Resolution|resolution]] 2.85&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'>[[2bx2]] is a 2 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=2BX2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BX2 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]] 2.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2bx2|  PDB=2bx2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bx2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bx2 OCA], [https://pdbe.org/2bx2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bx2 RCSB], [https://www.ebi.ac.uk/pdbsum/2bx2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bx2 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/bx/2bx2_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=2bx2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The coordinated regulation of gene expression is required for homeostasis, growth and development in all organisms. Such coordination may be partly achieved at the level of messenger RNA stability, in which the targeted destruction of subsets of transcripts generates the potential for cross-regulating metabolic pathways. In Escherichia coli, the balance and composition of the transcript population is affected by RNase E, an essential endoribonuclease that not only turns over RNA but also processes certain key RNA precursors. RNase E cleaves RNA internally, but its catalytic power is determined by the 5' terminus of the substrate, even if this lies at a distance from the cutting site. Here we report crystal structures of the catalytic domain of RNase E as trapped allosteric intermediates with RNA substrates. Four subunits of RNase E catalytic domain associate into an interwoven quaternary structure, explaining why the subunit organization is required for catalytic activity. The subdomain encompassing the active site is structurally congruent to a deoxyribonuclease, making an unexpected link in the evolutionary history of RNA and DNA nucleases. The structure explains how the recognition of the 5' terminus of the substrate may trigger catalysis and also sheds light on the question of how RNase E might selectively process, rather than destroy, specific RNA precursors.
-===CATALYTIC DOMAIN OF E. COLI RNASE E===
+Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover.,Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF Nature. 2005 Oct 20;437(7062):1187-91. PMID:16237448<ref>PMID:16237448</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2bx2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16237448}}, adds the Publication Abstract to the page
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16237448 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16237448}}
+__TOC__
+</StructureSection>
-==About this Structure==
-BX2 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=2BX2 OCA].
-==Reference==
-Structure of Escherichia coli RNase E catalytic domain and implications for RNA turnover., Callaghan AJ, Marcaida MJ, Stead JA, McDowall KJ, Scott WG, Luisi BF, Nature. 2005 Oct 20;437(7062):1187-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16237448 16237448]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Callaghan, A J.]]
+[[Category: Callaghan AJ]]
-[[Category: Luisi, B F.]]
+[[Category: Luisi BF]]
-[[Category: Marcaida, M J.]]
+[[Category: Marcaida MJ]]
-[[Category: Scott, W G.]]
+[[Category: Scott WG]]
-[[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 Mon Jul 28 10:04:01 2008''