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| | ==Structure of ribB complexed with inhibitor (4PEH) and metal ions== | | ==Structure of ribB complexed with inhibitor (4PEH) and metal ions== |
| - | <StructureSection load='4p6p' size='340' side='right' caption='[[4p6p]], [[Resolution|resolution]] 1.86Å' scene=''> | + | <StructureSection load='4p6p' size='340' side='right'caption='[[4p6p]], [[Resolution|resolution]] 1.86Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4p6p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibch Vibch]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P6P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P6P FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4p6p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae_O1_biovar_El_Tor_str._N16961 Vibrio cholerae O1 biovar El Tor str. N16961]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P6P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P6P FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RES:4-PHOSPHO-D-ERYTHRONOHYDROXAMIC+ACID'>RES</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]] 1.862Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4p6c|4p6c]], [[4p6d|4p6d]], [[4p77|4p77]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RES:4-PHOSPHO-D-ERYTHRONOHYDROXAMIC+ACID'>RES</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, VC_A1060 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243277 VIBCH])</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=4p6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p6p OCA], [https://pdbe.org/4p6p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p6p RCSB], [https://www.ebi.ac.uk/pdbsum/4p6p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p6p 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=4p6p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p6p OCA], [http://pdbe.org/4p6p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p6p RCSB], [http://www.ebi.ac.uk/pdbsum/4p6p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p6p ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RIBB_VIBCH RIBB_VIBCH]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. | + | [https://www.uniprot.org/uniprot/RIBB_VIBCH RIBB_VIBCH] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: 3,4-dihydroxy-2-butanone-4-phosphate synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Vibch]] | + | [[Category: Vibrio cholerae O1 biovar El Tor str. N16961]] |
| - | [[Category: Islam, Z]] | + | [[Category: Islam Z]] |
| - | [[Category: Karthikeyan, S]] | + | [[Category: Karthikeyan S]] |
| - | [[Category: Kumar, A]] | + | [[Category: Kumar A]] |
| - | [[Category: Salmon, L]] | + | [[Category: Salmon L]] |
| - | [[Category: Singh, S]] | + | [[Category: Singh S]] |
| - | [[Category: Complex]]
| + | |
| - | [[Category: Crystal]]
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| - | [[Category: Ligand]]
| + | |
| - | [[Category: Lyase-lyase inhibitor complex]]
| + | |
| - | [[Category: Ribb]]
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| - | [[Category: Riboflvain]]
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| Structural highlights
Function
RIBB_VIBCH Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.
Publication Abstract from PubMed
Riboflavin biosynthesis pathway has been shown to be essential in many pathogens and is absent in humans. Therefore, enzymes involved in riboflavin synthesis are considered as potential antibacterial drug targets. The enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) catalyzes one of the two committed steps in riboflavin pathway and converts D-ribulose-5-phosphate (Ru5P) to L-3,4-dihydroxy-2-butanone-4-phosphate and formate. Moreover, DHBPS is shown to be indispensable for Mycobacterium, Salmonella and Helicobacter species. Despite the essentiality of this enzyme in bacteria, no inhibitor has been identified hitherto. Here, we describe kinetic and crystal structure characterization of DHBPS from Vibrio cholerae (vDHBPS) with a competitive inhibitor 4-phospho-D-erythronohydroxamic acid (4PEH) at 1.86 A resolution. In addition, we also report the structural characterization of vDHBPS in its apo form, in complex with its substrate and substrate plus metal ions, at 1.96 A, 1.59 A and 2.04 A resolution, respectively. Comparison of these crystal structures suggests that 4PEH inhibits catalytic activity of DHBPS as it is unable to form a proposed intermediate which is crucial for DHBPS activity. Furthermore, vDHBPS structures complexed with substrate and metal ions reveal that unlike Candida albicans, binding of substrate to vDHBPS induces a conformational change from open to closed conformation. Interestingly, the position of second metal ion which is different from Methanococcus jannaschii strongly supports an active role in the catalytic mechanism. Thus, the kinetic and structural characterization of vDHBPS reveal the molecular mechanism of inhibition shown by 4PEH and it can be explored further for designing of novel antibiotics.
Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-Butanone-4-Phosphate Synthase from Vibrio cholerae.,Islam Z, Kumar A, Singh S, Salmon L, Karthikeyan S J Biol Chem. 2015 Mar 18. pii: jbc.M114.611830. PMID:25792735[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Islam Z, Kumar A, Singh S, Salmon L, Karthikeyan S. Structural Basis for Competitive Inhibition of 3,4-Dihydroxy-2-Butanone-4-Phosphate Synthase from Vibrio cholerae. J Biol Chem. 2015 Mar 18. pii: jbc.M114.611830. PMID:25792735 doi:http://dx.doi.org/10.1074/jbc.M114.611830
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