2fym: 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: @@
-[[Image:2fym.png|left|200px]]
-{{STRUCTURE_2fym|  PDB=2fym  |  SCENE=  }}
+==Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.==
+<StructureSection load='2fym' size='340' side='right'caption='[[2fym]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2fym]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FYM 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]] 1.6&#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></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=2fym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fym OCA], [https://pdbe.org/2fym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fym RCSB], [https://www.ebi.ac.uk/pdbsum/2fym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fym 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/fy/2fym_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=2fym ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In Escherichia coli, the glycolytic enzyme enolase is a component of the RNA degradosome, which is an RNase E mediated assembly involved in RNA processing and transcript turnover. The recruitment of enolase by the RNA degradosome has been implicated in the turnover of certain transcripts, and it is mediated by a small segment of roughly a dozen residues that lie within a natively unstructured sub-domain of RNase E. Here, we present the crystal structure of enolase in complex with its recognition site from RNase E at 1.6A resolution. A single molecule of the RNase E peptide binds asymmetrically in a conserved cleft at the interface of the enolase dimer. The recognition site is well conserved in RNase E homologues in a subfamily of the gamma-proteobacteria, including enzymes from pathogens such as Yersinia pestis, Vibrio cholera and Salmonella sp. We suggest that enolase is recruited into putative RNA degradosome machinery in these bacilli, where it plays common regulatory functions.
-===Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.===
+Recognition of enolase in the Escherichia coli RNA degradosome.,Chandran V, Luisi BF J Mol Biol. 2006 Apr 21;358(1):8-15. Epub 2006 Feb 21. PMID:16516921<ref>PMID:16516921</ref>
-{{ABSTRACT_PUBMED_16516921}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2fym" style="background-color:#fffaf0;"></div>
-[[2fym]] is a 6 chain structure with 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=2FYM OCA].
 ==See Also==
-*[[Enolase|Enolase]]
+*[[Enolase 3D structures|Enolase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016516921</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Phosphopyruvate hydratase]]
+[[Category: Escherichia coli K-12]]
-[[Category: Chandran, V.]]
+[[Category: Large Structures]]
-[[Category: Luisi, B F.]]
+[[Category: Chandran V]]
-[[Category: Enolase]]
+[[Category: Luisi BF]]
-[[Category: Lyase]]
-[[Category: Rna degradosome]]
-[[Category: Rnase e]]