6btg
From Proteopedia
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==Crystal structure of deoxyribose-phosphate aldolase bound with DHAP from Bacillus Thuringiensis== | ==Crystal structure of deoxyribose-phosphate aldolase bound with DHAP from Bacillus Thuringiensis== | ||
| - | <StructureSection load='6btg' size='340' side='right' caption='[[6btg]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='6btg' size='340' side='right'caption='[[6btg]], [[Resolution|resolution]] 1.70Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6btg]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6btg]] 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=6BTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BTG FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6btg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6btg OCA], [http://pdbe.org/6btg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6btg RCSB], [http://www.ebi.ac.uk/pdbsum/6btg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6btg 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=6btg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6btg OCA], [http://pdbe.org/6btg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6btg RCSB], [http://www.ebi.ac.uk/pdbsum/6btg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6btg 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 6btg" 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 bound with DHAP from Bacillus Thuringiensis
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