6kue - Revision history

OCA at 10:44, 27 March 2024

OCA — Wed, 27 Mar 2024 10:44:21 GMT

←Older revision		Revision as of 10:44, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6kue' size='340' side='right'caption='[[6kue]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='6kue' size='340' side='right'caption='[[6kue]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kue]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KUE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kue]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KUE FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SY94_3983 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~358~~ "~~Achromobacter radiobacter~~" ~~(Beijerinck and van Delden 1902) Bergey et al. 1934])</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]] 1.992Å</td></tr>
-	~~<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-ketoacyl~~-[~~acyl-carrier-protein]_synthase_I Beta-ketoacyl-~~[~~acyl-carrier-protein~~] ~~synthase I~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.~~1.~~41 2.3.1.41] </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=6kue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kue OCA], [https://pdbe.org/6kue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kue RCSB], [https://www.ebi.ac.uk/pdbsum/6kue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kue 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=6kue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kue OCA], [https://pdbe.org/6kue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kue RCSB], [https://www.ebi.ac.uk/pdbsum/6kue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kue ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A0F4FMM6_RHIRD A0A0F4FMM6_RHIRD]
-	Biotin is an essential micro-nutrient across the three domains of life. The paradigm earlier step of biotin synthesis denotes "BioC-BioH" pathway in Escherichia coli. Here we report that BioZ bypasses the canonical route to begin biotin synthesis. In addition to its origin of Rhizobiales, protein phylogeny infers that BioZ is domesticated to gain an atypical role of beta-ketoacyl-ACP synthase III. Genetic and biochemical characterization demonstrates that BioZ catalyzes the condensation of glutaryl-CoA (or ACP) with malonyl-ACP to give 5'-keto-pimeloyl ACP. This intermediate proceeds via type II fatty acid synthesis (FAS II) pathway, to initiate the formation of pimeloyl-ACP, a precursor of biotin synthesis. To further explore molecular basis of BioZ activity, we determine the crystal structure of Agrobacterium tumefaciens BioZ at 1.99 A, of which the catalytic triad and the substrate-loading tunnel are functionally defined. In particular, we localize that three residues (S84, R147, and S287) at the distant bottom of the tunnel might neutralize the charge of free C-carboxyl group of the primer glutaryl-CoA. Taken together, this study provides molecular insights into the BioZ biotin synthesis pathway.	+
-		+
-	Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway.,Zhang S, Xu Y, Guan H, Cui T, Liao Y, Wei W, Li J, Hassan BH, Zhang H, Jia X, Ouyang S, Feng Y Nat Commun. 2021 Apr 6;12(1):~~2056. doi: 10.1038~~/~~s41467-021-22360-4. PMID:33824341<ref>PMID:33824341<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6kue" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agrobacterium tumefaciens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hongxin, G]]	+	[[Category: Hongxin G]]
-	[[Category: Ouyang, S]]	+	[[Category: Ouyang S]]
-	[[Category: Sitao, Z]]	+	[[Category: Sitao Z]]
-	~~[[Category: Structure bioz]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:27, 21 April 2021

OCA — Wed, 21 Apr 2021 08:27:29 GMT

←Older revision		Revision as of 08:27, 21 April 2021
Line 8:		Line 8:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6kue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kue OCA], [https://pdbe.org/6kue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kue RCSB], [https://www.ebi.ac.uk/pdbsum/6kue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kue 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=6kue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kue OCA], [https://pdbe.org/6kue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kue RCSB], [https://www.ebi.ac.uk/pdbsum/6kue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kue ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biotin is an essential micro-nutrient across the three domains of life. The paradigm earlier step of biotin synthesis denotes "BioC-BioH" pathway in Escherichia coli. Here we report that BioZ bypasses the canonical route to begin biotin synthesis. In addition to its origin of Rhizobiales, protein phylogeny infers that BioZ is domesticated to gain an atypical role of beta-ketoacyl-ACP synthase III. Genetic and biochemical characterization demonstrates that BioZ catalyzes the condensation of glutaryl-CoA (or ACP) with malonyl-ACP to give 5'-keto-pimeloyl ACP. This intermediate proceeds via type II fatty acid synthesis (FAS II) pathway, to initiate the formation of pimeloyl-ACP, a precursor of biotin synthesis. To further explore molecular basis of BioZ activity, we determine the crystal structure of Agrobacterium tumefaciens BioZ at 1.99 A, of which the catalytic triad and the substrate-loading tunnel are functionally defined. In particular, we localize that three residues (S84, R147, and S287) at the distant bottom of the tunnel might neutralize the charge of free C-carboxyl group of the primer glutaryl-CoA. Taken together, this study provides molecular insights into the BioZ biotin synthesis pathway.
		+
		+	Biochemical and structural characterization of the BioZ enzyme engaged in bacterial biotin synthesis pathway.,Zhang S, Xu Y, Guan H, Cui T, Liao Y, Wei W, Li J, Hassan BH, Zhang H, Jia X, Ouyang S, Feng Y Nat Commun. 2021 Apr 6;12(1):2056. doi: 10.1038/s41467-021-22360-4. PMID:33824341<ref>PMID:33824341</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kue" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:50, 14 April 2021

OCA — Wed, 14 Apr 2021 06:50:01 GMT

←Older revision		Revision as of 06:50, 14 April 2021
Line 1:		Line 1:

	==The structure of BioZ from Agrobacterium tumefaciens==		==The structure of BioZ from Agrobacterium tumefaciens==
-	<StructureSection load='6kue' size='340' side='right'caption='[[6kue]]' scene=''>	+	<StructureSection load='6kue' size='340' side='right'caption='[[6kue]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KUE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KUE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kue]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KUE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KUE FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6kue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kue OCA], [~~http~~://pdbe.org/6kue PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kue RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kue PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kue ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SY94_3983 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-ketoacyl-[acyl-carrier-protein]_synthase_I Beta-ketoacyl-[acyl-carrier-protein] synthase I], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.41 2.3.1.41] </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=6kue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kue OCA], [https://pdbe.org/6kue PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kue RCSB], [https://www.ebi.ac.uk/pdbsum/6kue PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kue ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hongxin G]]	+	[[Category: Hongxin, G]]
-	[[Category: Ouyang S]]	+	[[Category: Ouyang, S]]
-	[[Category: Sitao Z]]	+	[[Category: Sitao, Z]]
		+	[[Category: Structure bioz]]
		+	[[Category: Transferase]]

OCA at 06:46, 2 September 2020

OCA — Wed, 02 Sep 2020 06:46:27 GMT

←Older revision		Revision as of 06:46, 2 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 6kue is ~~ON HOLD until Sep 01 2021~~	+	==The structure of BioZ from Agrobacterium tumefaciens==
-		+	<StructureSection load='6kue' size='340' side='right'caption='[[6kue]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KUE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KUE FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kue OCA], [http://pdbe.org/6kue PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kue RCSB], [http://www.ebi.ac.uk/pdbsum/6kue PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kue ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hongxin G]]
		+	[[Category: Ouyang S]]
		+	[[Category: Sitao Z]]

OCA at 02:28, 13 February 2020

OCA — Thu, 13 Feb 2020 02:28:04 GMT

←Older revision		Revision as of 02:28, 13 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kue is ON HOLD	+	The entry 6kue is ON HOLD until Sep 01 2021

	Authors:		Authors:

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

OCA — Wed, 02 Oct 2019 06:47:38 GMT

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

←Older revision

Revision as of 06:47, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6kue is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Oct 2019 06:47:36 GMT

New page: '''Unreleased structure''' The entry 6kue is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6kue is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]