2fym

From Proteopedia

(Difference between revisions)

Revision as of 15:36, 3 March 2021

Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.

Structural highlights

2fym is a 6 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1e9i
Gene:	eno ("Bacillus coli" Migula 1895)
Activity:	Phosphopyruvate hydratase, with EC number 4.2.1.11
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ENO_ECOLI] Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. It is also a component of the RNA degradosome, a multi-enzyme complex involved in RNA processing and messenger RNA degradation. Its interaction with RNase E is important for the turnover of mRNA, in particular on transcripts encoding enzymes of energy-generating metabolic routes. Its presence in the degradosome is required for the response to excess phosphosugar. May play a regulatory role in the degradation of specific RNAs, such as ptsG mRNA, therefore linking cellular metabolic status with post-translational gene regulation.^[1] ^[2] ^[3] [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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Py B, Higgins CF, Krisch HM, Carpousis AJ. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature. 1996 May 9;381(6578):169-72. PMID:8610017 doi:http://dx.doi.org/10.1038/381169a0
↑ Bernstein JA, Lin PH, Cohen SN, Lin-Chao S. Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2758-63. Epub 2004 Feb 23. PMID:14981237 doi:http://dx.doi.org/10.1073/pnas.0308747101
↑ Morita T, Kawamoto H, Mizota T, Inada T, Aiba H. Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Mol Microbiol. 2004 Nov;54(4):1063-75. PMID:15522087 doi:http://dx.doi.org/10.1111/j.1365-2958.2004.04329.x
↑ Chandran V, Luisi BF. Recognition of enolase in the Escherichia coli RNA degradosome. J Mol Biol. 2006 Apr 21;358(1):8-15. Epub 2006 Feb 21. PMID:16516921 doi:10.1016/j.jmb.2006.02.012

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2fym"

@@ Line 1: / Line 1: @@
 ==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=''>
+<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 [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FYM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fym]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1e9i|1e9i]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1e9i|1e9i]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">eno ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">eno ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphopyruvate_hydratase Phosphopyruvate hydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.11 4.2.1.11] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphopyruvate_hydratase Phosphopyruvate hydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.11 4.2.1.11] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fym OCA], [http://pdbe.org/2fym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fym RCSB], [http://www.ebi.ac.uk/pdbsum/2fym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fym ProSAT]</span></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 ==
-[[http://www.uniprot.org/uniprot/ENO_ECOLI ENO_ECOLI]] Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. It is also a component of the RNA degradosome, a multi-enzyme complex involved in RNA processing and messenger RNA degradation. Its interaction with RNase E is important for the turnover of mRNA, in particular on transcripts encoding enzymes of energy-generating metabolic routes. Its presence in the degradosome is required for the response to excess phosphosugar. May play a regulatory role in the degradation of specific RNAs, such as ptsG mRNA, therefore linking cellular metabolic status with post-translational gene regulation.<ref>PMID:8610017</ref> <ref>PMID:14981237</ref> <ref>PMID:15522087</ref>  [[http://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.
+[[https://www.uniprot.org/uniprot/ENO_ECOLI ENO_ECOLI]] Catalyzes the reversible conversion of 2-phosphoglycerate into phosphoenolpyruvate. It is essential for the degradation of carbohydrates via glycolysis. It is also a component of the RNA degradosome, a multi-enzyme complex involved in RNA processing and messenger RNA degradation. Its interaction with RNase E is important for the turnover of mRNA, in particular on transcripts encoding enzymes of energy-generating metabolic routes. Its presence in the degradosome is required for the response to excess phosphosugar. May play a regulatory role in the degradation of specific RNAs, such as ptsG mRNA, therefore linking cellular metabolic status with post-translational gene regulation.<ref>PMID:8610017</ref> <ref>PMID:14981237</ref> <ref>PMID:15522087</ref>  [[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>
+    <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>
@@ Line 31: / Line 31: @@
 </div>
 <div class="pdbe-citations 2fym" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Enolase 3D structures|Enolase 3D structures]]
 == References ==
 <references/>
@@ Line 36: / Line 39: @@
 </StructureSection>
 [[Category: Bacillus coli migula 1895]]
+[[Category: Large Structures]]
 [[Category: Phosphopyruvate hydratase]]
 [[Category: Chandran, V]]

2fym

From Proteopedia

Revision as of 15:36, 3 March 2021

Crystal structure of E. coli enolase complexed with the minimal binding segment of RNase E.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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