7sp3
From Proteopedia
(Difference between revisions)
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==E. coli RppH bound to Ap4A== | ==E. coli RppH bound to Ap4A== | ||
| - | <StructureSection load='7sp3' size='340' side='right'caption='[[7sp3]]' scene=''> | + | <StructureSection load='7sp3' size='340' side='right'caption='[[7sp3]], [[Resolution|resolution]] 1.60Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7SP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SP3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7sp3]] is a 1 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=7SP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7SP3 FirstGlance]. <br> |
| - | </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=7sp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sp3 OCA], [https://pdbe.org/7sp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7sp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sp3 ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B4P:BIS(ADENOSINE)-5-TETRAPHOSPHATE'>B4P</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <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=7sp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7sp3 OCA], [https://pdbe.org/7sp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7sp3 RCSB], [https://www.ebi.ac.uk/pdbsum/7sp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7sp3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RPPH_ECOLI RPPH_ECOLI] Master regulator of 5'-dependent mRNA decay. Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Preferentially hydrolyzes diadenosine penta-phosphate with ATP as one of the reaction products. Also able to hydrolyze diadenosine hexa- and tetra-phosphate. Has no activity on diadenosine tri-phosphate, ADP-ribose, NADH and UDP-glucose. In the meningitis causing strain E.coli K1, has been shown to play a role in HBMEC (human brain microvascular endothelial cells) invasion in vitro.<ref>PMID:10760174</ref> <ref>PMID:18202662</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Dinucleoside tetraphosphates, often described as alarmones because their cellular concentration increases in response to stress, have recently been shown to function in bacteria as precursors to nucleoside tetraphosphate (Np4) RNA caps. Removal of this cap is critical for initiating 5' end-dependent degradation of those RNAs, potentially affecting bacterial adaptability to stress; however, the predominant Np4 decapping enzyme in proteobacteria, ApaH, is inactivated by the very conditions of disulfide stress that enable Np4-capped RNAs to accumulate to high levels. Here, we show that, in Escherichia coli cells experiencing such stress, the RNA pyrophosphohydrolase RppH assumes a leading role in decapping those transcripts, preferring them as substrates over their triphosphorylated and diphosphorylated counterparts. Unexpectedly, this enzyme recognizes Np4-capped 5' ends by a mechanism distinct from the one it uses to recognize other 5' termini, resulting in a one-nucleotide shift in substrate specificity. The unique manner in which capped substrates of this kind bind to the active site of RppH positions the delta-phosphate, rather than the beta-phosphate, for hydrolytic attack, generating triphosphorylated RNA as the primary product of decapping. Consequently, a second RppH-catalyzed deprotection step is required to produce the monophosphorylated 5' terminus needed to stimulate rapid RNA decay. The unconventional manner in which RppH recognizes Np4-capped 5' ends and its differential impact on the rates at which such termini are deprotected as a prelude to RNA degradation could have major consequences for reprogramming gene expression during disulfide stress. | ||
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| + | A distinct RNA recognition mechanism governs Np4 decapping by RppH.,Levenson-Palmer R, Luciano DJ, Vasilyev N, Nuthanakanti A, Serganov A, Belasco JG Proc Natl Acad Sci U S A. 2022 Feb 8;119(6). pii: 2117318119. doi:, 10.1073/pnas.2117318119. PMID:35131855<ref>PMID:35131855</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7sp3" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Escherichia coli]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Nuthanakanti A]] | [[Category: Nuthanakanti A]] | ||
[[Category: Serganov AA]] | [[Category: Serganov AA]] | ||
[[Category: Vasilyev N]] | [[Category: Vasilyev N]] | ||
Current revision
E. coli RppH bound to Ap4A
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