6btd: Difference between revisions
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New page: '''Unreleased structure''' The entry 6btd is ON HOLD Authors: Li, Q., Bruner, S.D. Description: Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved... |
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The | ==Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose== | ||
<StructureSection load='6btd' size='340' side='right'caption='[[6btd]], [[Resolution|resolution]] 1.55Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6btd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thuringiensis Bacillus thuringiensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BTD 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]] 1.551Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6btd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6btd OCA], [https://pdbe.org/6btd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6btd RCSB], [https://www.ebi.ac.uk/pdbsum/6btd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6btd ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A231I520_BACTU A0A231I520_BACTU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
5-Deoxyribose is formed from 5'-deoxyadenosine, a toxic byproduct of radical S-adenosylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown. Here, we define a salvage pathway for 5-deoxyribose in bacteria, consisting of phosphorylation, isomerization, and aldol cleavage steps. Analysis of bacterial genomes uncovers widespread, unassigned three-gene clusters specifying a putative kinase, isomerase, and sugar phosphate aldolase. We show that the enzymes encoded by the Bacillus thuringiensis cluster, acting together in vitro, convert 5-deoxyribose successively to 5-deoxyribose 1-phosphate, 5-deoxyribulose 1-phosphate, and dihydroxyacetone phosphate plus acetaldehyde. Deleting the isomerase decreases the 5-deoxyribulose 1-phosphate pool size, and deleting either the isomerase or the aldolase increases susceptibility to 5-deoxyribose. The substrate preference of the aldolase is unique among family members, and the X-ray structure reveals an unusual manganese-dependent enzyme. This work defines a salvage pathway for 5-deoxyribose, a near-universal metabolite. | |||
Salvage of the 5-deoxyribose byproduct of radical SAM enzymes.,Beaudoin GAW, Li Q, Folz J, Fiehn O, Goodsell JL, Angerhofer A, Bruner SD, Hanson AD Nat Commun. 2018 Aug 6;9(1):3105. doi: 10.1038/s41467-018-05589-4. PMID:30082730<ref>PMID:30082730</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6btd" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
==See Also== | |||
*[[Aldolase 3D structures|Aldolase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus thuringiensis]] | |||
[[Category: Large Structures]] | |||
[[Category: Bruner SD]] | |||
[[Category: Li Q]] | |||
Latest revision as of 14:49, 4 October 2023
Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose
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