6btd - Revision history

OCA at 14:49, 4 October 2023

OCA — Wed, 04 Oct 2023 14:49:53 GMT

←Older revision		Revision as of 14:49, 4 October 2023
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	<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 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>	+	<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='~~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='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='~~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='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~~='~~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'>[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>
-	<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>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A231I520_BACTU A0A231I520_BACTU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~cereus var.~~ thuringiensis ~~smith et al. 1952]]~~	+	[[Category: Bacillus thuringiensis]]
-	~~[[Category: L-fuculose-phosphate aldolase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bruner~~, S D~~]]	+	[[Category: Bruner SD]]
-	[[Category: Li, Q]]	+	[[Category: Li Q]]
-	~~[[Category: 5-deoxyribose]]~~	+
-	~~[[Category: Aldolase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Radical sam enzyme byproduct~~]]	+

OCA at 13:21, 10 May 2019

OCA — Fri, 10 May 2019 13:21:42 GMT

←Older revision		Revision as of 13:21, 10 May 2019
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	==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]]

OCA at 07:11, 4 July 2018

OCA — Wed, 04 Jul 2018 07:11:44 GMT

←Older revision		Revision as of 07:11, 4 July 2018
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-	'''Unreleased structure'''

-	~~The entry 6btd is ON HOLD until Paper Publication~~	+	==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=''>
-	~~Authors: Li, Q., Bruner, S.D.~~	+	== 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>
-	~~Description:~~ Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<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>
-	[[Category: Bruner, S.D]]	+	<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>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: L-fuculose-phosphate aldolase]]
		+	[[Category: Bruner, S D]]
	[[Category: Li, Q]]		[[Category: Li, Q]]
		+	[[Category: 5-deoxyribose]]
		+	[[Category: Aldolase]]
		+	[[Category: Lyase]]
		+	[[Category: Radical sam enzyme byproduct]]

OCA at 05:39, 17 January 2018

OCA — Wed, 17 Jan 2018 05:39:44 GMT

←Older revision		Revision as of 05:39, 17 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6btd is ON HOLD	+	The entry 6btd is ON HOLD until Paper Publication

	Authors: Li, Q., Bruner, S.D.		Authors: Li, Q., Bruner, S.D.
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	Description: Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose		Description: Crystal structure of deoxyribose-phosphate aldolase from Bacillus Thuringiensis involved in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Li, Q]]
	[[Category: Bruner, S.D]]		[[Category: Bruner, S.D]]
		+	[[Category: Li, Q]]

OCA: Protected "6btd" [edit=sysop:move=sysop]

OCA — Wed, 13 Dec 2017 05:56:44 GMT

Protected "6btd" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:56, 13 December 2017

OCA: 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...

OCA — Wed, 13 Dec 2017 05:56:42 GMT

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...

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 in dispatching the ubiquitous radical SAM enzyme byproduct 5-deoxyribose
[[Category: Unreleased Structures]]
[[Category: Li, Q]]
[[Category: Bruner, S.D]]