This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
6btd
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
==Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose== | ==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=''> | + | <StructureSection load='6btd' size='340' side='right'caption='[[6btd]], [[Resolution|resolution]] 1.55Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6btd]] is a 1 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6btd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_cereus_var._thuringiensis"_smith_et_al._1952 "bacillus cereus var. thuringiensis" smith et al. 1952]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTD FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BK775_23715, CCZ40_07290 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1428 "Bacillus cereus var. thuringiensis" Smith et al. 1952])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-fuculose-phosphate_aldolase L-fuculose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.17 4.1.2.17] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-fuculose-phosphate_aldolase L-fuculose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.17 4.1.2.17] </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=6btd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6btd OCA], [http://pdbe.org/6btd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6btd RCSB], [http://www.ebi.ac.uk/pdbsum/6btd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6btd ProSAT]</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=6btd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6btd OCA], [http://pdbe.org/6btd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6btd RCSB], [http://www.ebi.ac.uk/pdbsum/6btd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6btd ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <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> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6btd" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Aldolase 3D structures|Aldolase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacillus cereus var. thuringiensis smith et al. 1952]] | ||
[[Category: L-fuculose-phosphate aldolase]] | [[Category: L-fuculose-phosphate aldolase]] | ||
| + | [[Category: Large Structures]] | ||
[[Category: Bruner, S D]] | [[Category: Bruner, S D]] | ||
[[Category: Li, Q]] | [[Category: Li, Q]] | ||
Revision as of 13:21, 10 May 2019
Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose
| |||||||||||
