7uf1 - Revision history

OCA at 17:14, 18 October 2023

OCA — Wed, 18 Oct 2023 17:14:54 GMT

←Older revision		Revision as of 17:14, 18 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7uf1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7uf1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF1 FirstGlance]. <br>
-	</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=R5P:RIBOSE-5-PHOSPHATE'>R5P</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]] 1.95Å</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=R5P:RIBOSE-5-PHOSPHATE'>R5P</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=7uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf1 OCA], [https://pdbe.org/7uf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf1 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=7uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf1 OCA], [https://pdbe.org/7uf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A0H6NPW4_VIBCL A0A0H6NPW4_VIBCL]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.[ARBA:ARBA00002284][HAMAP-Rule:MF_00180][RuleBase:RU003843]	+	[https://www.uniprot.org/uniprot/A0A0H6NPW4_VIBCL A0A0H6NPW4_VIBCL] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.[ARBA:ARBA00002284][HAMAP-Rule:MF_00180][RuleBase:RU003843]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 03:55, 8 September 2022

OCA — Thu, 08 Sep 2022 03:55:52 GMT

←Older revision		Revision as of 03:55, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7uf1' size='340' side='right'caption='[[7uf1]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='7uf1' size='340' side='right'caption='[[7uf1]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7uf1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7uf1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF1 FirstGlance]. <br>
	</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=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>		</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=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3,4-dihydroxy-2-butanone-4-phosphate_synthase 3,4-dihydroxy-2-butanone-4-phosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.12 4.1.99.12] </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=7uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf1 OCA], [https://pdbe.org/7uf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf1 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=7uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf1 OCA], [https://pdbe.org/7uf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A0H6NPW4_VIBCL A0A0H6NPW4_VIBCL]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.[ARBA:ARBA00002284][HAMAP-Rule:MF_00180][RuleBase:RU003843]	+	[[https://www.uniprot.org/uniprot/A0A0H6NPW4_VIBCL A0A0H6NPW4_VIBCL]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.[ARBA:ARBA00002284][HAMAP-Rule:MF_00180][RuleBase:RU003843]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3,4-dihydroxy-2-butanone-4-phosphate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kenjic, N~~]]	+	[[Category: Vibrio cholerae]]
-	[[Category: ~~Lamb, A L~~]]	+	[[Category: Kenjic N]]
-	[[Category: ~~Meneely, K M~~]]	+	[[Category: Lamb AL]]
-	[[Category: ~~4-dihydroxy-2-butanone 4-phosphate synthase]]~~	+	[[Category: Meneely KM]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Ribb]]~~	+
-	~~[[Category: Riboflavin~~]]	+

OCA at 05:03, 3 August 2022

OCA — Wed, 03 Aug 2022 05:03:08 GMT

←Older revision		Revision as of 05:03, 3 August 2022
Line 1:		Line 1:

	==RibB from Vibrio cholera bound with D-Ribose-5-phosphate (D-R5P) and manganese==		==RibB from Vibrio cholera bound with D-Ribose-5-phosphate (D-R5P) and manganese==
-	<StructureSection load='7uf1' size='340' side='right'caption='[[7uf1]]' scene=''>	+	<StructureSection load='7uf1' size='340' side='right'caption='[[7uf1]], [[Resolution\|resolution]] 1.95Å' 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=7UF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7uf1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF1 FirstGlance]. <br>
-	</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=7uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf1 OCA], [https://pdbe.org/7uf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf1 ProSAT]</span></td></tr>	+	</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=R5P:RIBOSE-5-PHOSPHATE'>R5P</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3,4-dihydroxy-2-butanone-4-phosphate_synthase 3,4-dihydroxy-2-butanone-4-phosphate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.12 4.1.99.12] </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=7uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf1 OCA], [https://pdbe.org/7uf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A0H6NPW4_VIBCL A0A0H6NPW4_VIBCL]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.[ARBA:ARBA00002284][HAMAP-Rule:MF_00180][RuleBase:RU003843]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RibB (3,4-dihydroxy-2-butanone 4-phosphate synthase) is a magnesium-dependent enzyme that excises the C4 of d-ribulose-5-phosphate (d-Ru5P) as formate. RibB generates the four-carbon substrate for lumazine synthase that is incorporated into the xylene moiety of lumazine and ultimately the riboflavin isoalloxazine. The reaction was first identified by Bacher and co-workers in the 1990s, and their chemical mechanism hypothesis became canonical despite minimal direct evidence. X-ray crystal structures of RibB typically show two metal ions when solved in the presence of non-native metals and/or liganding non-substrate analogues, and the consensus hypothetical mechanism has incorporated this cofactor set. We have used a variety of biochemical approaches to further characterize the chemistry catalyzed by RibB from Vibrio cholera (VcRibB). We show that full activity is achieved at metal ion concentrations equal to the enzyme concentration. This was confirmed by electron paramagnetic resonance of the enzyme reconstituted with manganese and crystal structures liganded with Mn(2+) and a variety of sugar phosphates. Two transient species prior to the formation of products were identified using acid quench of single turnover reactions in combination with NMR for singly and fully (13)C-labeled d-Ru5P. These data indicate that dehydration of C1 forms the first transient species, which undergoes rearrangement by a 1,2 migration, fusing C5 to C3 and generating a hydrated C4 that is poised for elimination as formate. Structures determined from time-dependent Mn(2+) soaks of VcRibB-d-Ru5P crystals show accumulation in crystallo of the same intermediates. Collectively, these data reveal for the first time crucial transient chemical states in the mechanism of RibB.
		+
		+	Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis.,Kenjic N, Meneely KM, Wherritt DJ, Denler MC, Jackson TA, Moran GR, Lamb AL J Am Chem Soc. 2022 Jul 20;144(28):12769-12780. doi: 10.1021/jacs.2c03376. Epub, 2022 Jul 8. PMID:35802469<ref>PMID:35802469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7uf1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 3,4-dihydroxy-2-butanone-4-phosphate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kenjic N]]	+	[[Category: Kenjic, N]]
-	[[Category: Lamb AL]]	+	[[Category: Lamb, A L]]
-	[[Category: Meneely KM]]	+	[[Category: Meneely, K M]]
		+	[[Category: 4-dihydroxy-2-butanone 4-phosphate synthase]]
		+	[[Category: Lyase]]
		+	[[Category: Ribb]]
		+	[[Category: Riboflavin]]

OCA at 06:52, 20 July 2022

OCA — Wed, 20 Jul 2022 06:52:50 GMT

←Older revision		Revision as of 06:52, 20 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7uf1 is ON HOLD until Paper Publication~~	+	==RibB from Vibrio cholera bound with D-Ribose-5-phosphate (D-R5P) and manganese==
-		+	<StructureSection load='7uf1' size='340' side='right'caption='[[7uf1]]' scene=''>
-	~~Authors: Kenjic, N., Meneely, K.M., Lamb, A.L.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF1 FirstGlance]. <br>
-	~~Description:~~ RibB from Vibrio cholera bound with D-Ribose-5-phosphate (D-R5P) and manganese	+	</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=7uf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf1 OCA], [https://pdbe.org/7uf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf1 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Lamb~~, A.L]]	+	__TOC__
-	[[Category: ~~Meneely, K.M~~]]	+	</StructureSection>
-	[[Category: Kenjic, N]]	+	[[Category: Large Structures]]
		+	[[Category: Kenjic N]]
		+	[[Category: Lamb AL]]
		+	[[Category: Meneely KM]]

OCA: Protected "7uf1" [edit=sysop:move=sysop]

OCA — Wed, 30 Mar 2022 09:35:02 GMT

Protected "7uf1" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:35, 30 March 2022

OCA: New page: '''Unreleased structure''' The entry 7uf1 is ON HOLD until Paper Publication Authors: Kenjic, N., Meneely, K.M., Lamb, A.L. Description: RibB from Vibrio cholera bound with D-Ribose-5-...

OCA — Wed, 30 Mar 2022 09:34:59 GMT

New page: '''Unreleased structure''' The entry 7uf1 is ON HOLD until Paper Publication Authors: Kenjic, N., Meneely, K.M., Lamb, A.L. Description: RibB from Vibrio cholera bound with D-Ribose-5-...

New page

'''Unreleased structure'''

The entry 7uf1 is ON HOLD until Paper Publication

Authors: Kenjic, N., Meneely, K.M., Lamb, A.L.

Description: RibB from Vibrio cholera bound with D-Ribose-5-phosphate (D-R5P) and manganese
[[Category: Unreleased Structures]]
[[Category: Lamb, A.L]]
[[Category: Meneely, K.M]]
[[Category: Kenjic, N]]