6d13: Difference between revisions
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==Crystal structure of E.coli RppH-DapF complex== | ==Crystal structure of E.coli RppH-DapF complex== | ||
<StructureSection load='6d13' size='340' side='right' caption='[[6d13]], [[Resolution|resolution]] 3.06Å' scene=''> | <StructureSection load='6d13' size='340' side='right'caption='[[6d13]], [[Resolution|resolution]] 3.06Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6d13]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6d13]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_S88 Escherichia coli S88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6D13 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6D13 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.06Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=6d13 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6d13 OCA], [https://pdbe.org/6d13 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6d13 RCSB], [https://www.ebi.ac.uk/pdbsum/6d13 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6d13 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/DAPF_ECOLI DAPF_ECOLI] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Only accepts DAP isomers with the L configuration.<ref>PMID:6378903</ref> <ref>PMID:3031013</ref> <ref>PMID:3042781</ref> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Escherichia coli S88]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Gao | [[Category: Gao A]] | ||
[[Category: Serganov | [[Category: Serganov A]] | ||
Latest revision as of 18:15, 4 October 2023
Crystal structure of E.coli RppH-DapF complexCrystal structure of E.coli RppH-DapF complex
Structural highlights
FunctionDAPF_ECOLI Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Only accepts DAP isomers with the L configuration.[1] [2] [3] Publication Abstract from PubMedVitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5' termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5'-end-dependent mRNA degradation begins with the generation of monophosphorylated 5' termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis. We have determined crystal structures of RppH-DapF complexes and measured rates of RNA deprotection. These studies show that DapF potentiates RppH activity in two ways, depending on the nature of the substrate. Its stimulatory effect on the reactivity of diphosphorylated RNAs, the predominant natural substrates of RppH, requires a substrate long enough to reach DapF in the complex, while the enhanced reactivity of triphosphorylated RNAs appears to involve DapF-induced changes in RppH itself and likewise increases with substrate length. This study provides a basis for understanding the intricate relationship between cellular metabolism and mRNA decay and reveals striking parallels with the stimulation of decapping activity in eukaryotes. Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.,Gao A, Vasilyev N, Luciano DJ, Levenson-Palmer R, Richards J, Marsiglia WM, Traaseth NJ, Belasco JG, Serganov A Nucleic Acids Res. 2018 May 4. pii: 4992646. doi: 10.1093/nar/gky327. PMID:29733359[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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