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| | <StructureSection load='3ahf' size='340' side='right'caption='[[3ahf]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='3ahf' size='340' side='right'caption='[[3ahf]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ahf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bifidobacterium_parvulorum"_reuter_1963 "bifidobacterium parvulorum" reuter 1963]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AHF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ahf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_breve Bifidobacterium breve]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AHF FirstGlance]. <br> |
| - | </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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ahc|3ahc]], [[3ahd|3ahd]], [[3ahe|3ahe]], [[3ahg|3ahg]], [[3ahh|3ahh]], [[3ahi|3ahi]], [[3ahj|3ahj]]</div></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=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xfp ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1685 "Bifidobacterium parvulorum" Reuter 1963])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Fructose-6-phosphate_phosphoketolase Fructose-6-phosphate phosphoketolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.22 4.1.2.22] </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=3ahf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ahf OCA], [https://pdbe.org/3ahf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ahf RCSB], [https://www.ebi.ac.uk/pdbsum/3ahf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ahf 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=3ahf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ahf OCA], [https://pdbe.org/3ahf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ahf RCSB], [https://www.ebi.ac.uk/pdbsum/3ahf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ahf ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/D6PAH1_BIFBR D6PAH1_BIFBR] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bifidobacterium parvulorum reuter 1963]] | + | [[Category: Bifidobacterium breve]] |
| - | [[Category: Fructose-6-phosphate phosphoketolase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ashida, H]] | + | [[Category: Ashida H]] |
| - | [[Category: Fushinobu, S]] | + | [[Category: Fushinobu S]] |
| - | [[Category: Katayama, T]] | + | [[Category: Katayama T]] |
| - | [[Category: Kim, B J]] | + | [[Category: Kim B-J]] |
| - | [[Category: Shoun, H]] | + | [[Category: Shoun H]] |
| - | [[Category: Suzuki, R]] | + | [[Category: Suzuki R]] |
| - | [[Category: Wakagi, T]] | + | [[Category: Wakagi T]] |
| - | [[Category: Yamamoto, K]] | + | [[Category: Yamamoto K]] |
| - | [[Category: Alpha-beta fold]]
| + | |
| - | [[Category: Homodimer]]
| + | |
| - | [[Category: Inorganic phosphate]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Thiamine diphosphate-dependent enzyme]]
| + | |
| Structural highlights
Function
D6PAH1_BIFBR
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
Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bacteria and in the pentose catabolism of various microbes. In particular, bifidobacteria, representatives of beneficial commensal bacteria, have an effective glycolytic pathway called bifid shunt in which 2.5 mol of ATP are produced per glucose. Phosphoketolase catalyzes two steps in the bifid shunt because of its dual-substrate specificity; they are phosphorolytic cleavage of fructose 6-phosphate or xylulose 5-phosphate to produce aldose phosphate, acetyl phosphate, and H(2)O. The phosphoketolase reaction is different from other well studied ThDP-dependent enzymes because it involves a dehydration step. Although phosphoketolase was discovered more than 50 years ago, its three-dimensional structure remains unclear. In this study we report the crystal structures of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase from Bifidobacterium breve. The structures of the two intermediates before and after dehydration (alpha,beta-dihydroxyethyl ThDP and 2-acetyl-ThDP) and complex with inorganic phosphate give an insight into the mechanism of each step of the enzymatic reaction.
Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism.,Suzuki R, Katayama T, Kim BJ, Wakagi T, Shoun H, Ashida H, Yamamoto K, Fushinobu S J Biol Chem. 2010 Oct 29;285(44):34279-87. Epub 2010 Aug 24. PMID:20739284[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Suzuki R, Katayama T, Kim BJ, Wakagi T, Shoun H, Ashida H, Yamamoto K, Fushinobu S. Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism. J Biol Chem. 2010 Oct 29;285(44):34279-87. Epub 2010 Aug 24. PMID:20739284 doi:10.1074/jbc.M110.156281
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