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7uf5

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Current revision

RibB from Vibrio cholera bound with intermediate 2 in the reaction cycle and the products DHBP and formate

Structural highlights

7uf5 is a 1 chain structure with sequence from Vibrio cholerae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kenjic N, Meneely KM, Wherritt DJ, Denler MC, Jackson TA, Moran GR, Lamb AL. Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis. J Am Chem Soc. 2022 Jul 20;144(28):12769-12780. doi: 10.1021/jacs.2c03376. Epub, 2022 Jul 8. PMID:35802469 doi:http://dx.doi.org/10.1021/jacs.2c03376

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7uf5"

Categories: Large Structures | Vibrio cholerae | Kenjic N | Lamb AL | Meneely KM

@@ Line 3: / Line 3: @@
 <StructureSection load='7uf5' size='340' side='right'caption='[[7uf5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7uf5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7uf5]] 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=7UF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UF5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=N4O:(2R)-2-hydroxy-3-oxobutyl+dihydrogen+phosphate'>N4O</scene>, <scene name='pdbligand=N52:(2R)-2-(dihydroxymethyl)-2-hydroxy-3-oxobutyl+dihydrogen+phosphate'>N52</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]] 2.1&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=N4O:(2R)-2-hydroxy-3-oxobutyl+dihydrogen+phosphate'>N4O</scene>, <scene name='pdbligand=N52:(2R)-2-(dihydroxymethyl)-2-hydroxy-3-oxobutyl+dihydrogen+phosphate'>N52</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=7uf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7uf5 OCA], [https://pdbe.org/7uf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7uf5 RCSB], [https://www.ebi.ac.uk/pdbsum/7uf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7uf5 ProSAT]</span></td></tr>
 </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]
+[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 ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: 3,4-dihydroxy-2-butanone-4-phosphate synthase]]
 [[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]]

7uf5

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Current revision

RibB from Vibrio cholera bound with intermediate 2 in the reaction cycle and the products DHBP and formate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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