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3ls6

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Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate and zinc

Structural highlights

3ls6 is a 2 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.86Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RIBB_SALTY Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

3,4-Dihydroxy-2-butanone-4-phosphate synthase (DHBPS) encoded by ribB gene is one of the first enzymes in riboflavin biosynthesis pathway and catalyzes the conversion of ribulose-5-phosphate (Ru5P) to 3,4-dihydroxy-2-butanone-4-phosphate and formate. DHBPS is an attractive target for developing anti-bacterial drugs as this enzyme is essential for pathogens, but absent in humans. The recombinant DHBPS enzyme of Salmonella requires magnesium ion for its activity and catalyzes the formation of 3,4-dihydroxy-2-butanone-4-phosphate from Ru5P at a rate of 199 nmol min(-1) mg(-1) with K(m) value of 116 muM at 37 degrees C. Further, we have determined the crystal structures of Salmonella DHBPS in complex with sulfate, Ru5P and sulfate-zinc ion at a resolution of 2.80, 2.52, and 1.86 A, respectively. Analysis of these crystal structures reveals that the acidic loop (residues 34-39) responsible for the acid-base catalysis is disordered in the absence of substrate or metal ion at the active site. Upon binding either substrate or sulfate and metal ions, the acidic loop becomes stabilized, adopts a closed conformation and interacts with the substrate. Our structure for the first time reveals that binding of substrate Ru5P alone is sufficient for the stabilization of the acidic active site loop into a closed conformation. In addition, the Glu38 residue from the acidic active site loop undergoes a conformational change upon Ru5P binding, which helps in positioning the second metal ion that stabilizes the Ru5P and the reaction intermediates. This is the first structural report of DHBPS in complex with either substrate or metal ion from any eubacteria. Proteins 2010. (c) 2010 Wiley-Liss, Inc.

Potential anti-bacterial drug target: Structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2.,Kumar P, Singh M, Gautam R, Karthikeyan S Proteins. 2010 Jul 30. PMID:20806221^[1]

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

References

↑ Kumar P, Singh M, Gautam R, Karthikeyan S. Potential anti-bacterial drug target: Structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2. Proteins. 2010 Jul 30. PMID:20806221 doi:10.1002/prot.22837

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ls6"

Categories: Large Structures | Salmonella enterica subsp. enterica serovar Typhimurium | Karthikeyan S | Kumar P

@@ Line 1: / Line 1: @@
 ==Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate and zinc==
-<StructureSection load='3ls6' size='340' side='right' caption='[[3ls6]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
+<StructureSection load='3ls6' size='340' side='right'caption='[[3ls6]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ls6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LS6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ls6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LS6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.86&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lqu|3lqu]], [[3lrj|3lrj]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ribB, STM3195 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</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=3ls6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ls6 OCA], [https://pdbe.org/3ls6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ls6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ls6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ls6 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3,4-dihydroxy-2-butanone-4-phosphate_synthase 3,4-dihydroxy-2-butanone-4-phosphate synthase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ls6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ls6 OCA], [http://pdbe.org/3ls6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ls6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ls6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ls6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RIBB_SALTY RIBB_SALTY]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate (By similarity).
+[https://www.uniprot.org/uniprot/RIBB_SALTY RIBB_SALTY] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ls/3ls6_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ls/3ls6_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus typhimurium loeffler 1892]]
+[[Category: Large Structures]]
-[[Category: 3,4-dihydroxy-2-butanone-4-phosphate synthase]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Karthikeyan, S]]
+[[Category: Karthikeyan S]]
-[[Category: Kumar, P]]
+[[Category: Kumar P]]
-[[Category: Antibacterial]]
-[[Category: Dhbp]]
-[[Category: Dimetal center]]
-[[Category: Drug target]]
-[[Category: Lyase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Riboflavin biosynthesis]]

3ls6

From Proteopedia

Current revision

Crystal structure of 3,4-Dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate and zinc

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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