3eeu
From Proteopedia
(Difference between revisions)
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<StructureSection load='3eeu' size='340' side='right'caption='[[3eeu]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='3eeu' size='340' side='right'caption='[[3eeu]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[3eeu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[3eeu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bdellovibrio_bacteriovorus Bdellovibrio bacteriovorus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EEU 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]] 2Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HO:HOLMIUM+ATOM'>HO</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=3eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eeu OCA], [https://pdbe.org/3eeu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eeu RCSB], [https://www.ebi.ac.uk/pdbsum/3eeu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eeu 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=3eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eeu OCA], [https://pdbe.org/3eeu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eeu RCSB], [https://www.ebi.ac.uk/pdbsum/3eeu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eeu ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q6MPX4_BDEBA Q6MPX4_BDEBA] | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=3eeu ConSurf]. | </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=3eeu ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Until recently, the mechanism of mRNA decay in bacteria was thought to be different from that of eukaryotes. This paradigm changed with the discovery that RppH (ORF176/NudH/YgdP), an Escherichia coli enzyme that belongs to the Nudix superfamily, is an RNA pyrophosphohydrolase that initiates mRNA decay by cleaving pyrophosphate from the 5'-triphosphate. Here we report the 1.9 Angstroms resolution structure of the Nudix hydrolase BdRppH from Bdellovibrio bacteriovorus, a bacterium that feeds on other Gram-negative bacteria. Based on the structure of the enzyme alone and in complex with GTP-Mg2+, we propose a mode of RNA binding similar to that of the nuclear decapping enzyme from Xenopus laevis, X29. In additional experiments, we show that BdRppH can indeed function in vitro and in vivo as an RNA pyrophosphohydrolase. These findings set the basis for the identification of possible decapping enzymes in other bacteria. | ||
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| - | Structure and biological function of the RNA pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.,Messing SA, Gabelli SB, Liu Q, Celesnik H, Belasco JG, Pineiro SA, Amzel LM Structure. 2009 Mar 11;17(3):472-81. PMID:19278661<ref>PMID:19278661</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 3eeu" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Bdellovibrio bacteriovorus]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Amzel | + | [[Category: Amzel LM]] |
| - | [[Category: Gabelli | + | [[Category: Gabelli SB]] |
| - | [[Category: Messing | + | [[Category: Messing SA]] |
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Current revision
Structure of the RNA pyrophosphohydrolase BdRppH in complex with Holmium
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