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| | ==3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate== | | ==3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate== |
| - | <StructureSection load='1pvy' size='340' side='right' caption='[[1pvy]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='1pvy' size='340' side='right'caption='[[1pvy]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1pvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PVY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1pvy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PVY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5RP:RIBULOSE-5-PHOSPHATE'>5RP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pvw|1pvw]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5RP:RIBULOSE-5-PHOSPHATE'>5RP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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">MJ0055 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=1pvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvy OCA], [https://pdbe.org/1pvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pvy RCSB], [https://www.ebi.ac.uk/pdbsum/1pvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvy ProSAT]</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=1pvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvy OCA], [http://pdbe.org/1pvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pvy RCSB], [http://www.ebi.ac.uk/pdbsum/1pvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RIBB_METJA RIBB_METJA]] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.<ref>PMID:12200440</ref> | + | [https://www.uniprot.org/uniprot/RIBB_METJA RIBB_METJA] Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.<ref>PMID:12200440</ref> |
| | == 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: Atcc 43067]] | + | [[Category: Large Structures]] |
| - | [[Category: Bacher, A]] | + | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Fischer, M]] | + | [[Category: Bacher A]] |
| - | [[Category: Huber, R]] | + | [[Category: Fischer M]] |
| - | [[Category: Richter, G]] | + | [[Category: Huber R]] |
| - | [[Category: Schiffmann, S]] | + | [[Category: Richter G]] |
| - | [[Category: Steinbacher, S]] | + | [[Category: Schiffmann S]] |
| - | [[Category: Isomerase]]
| + | [[Category: Steinbacher S]] |
| - | [[Category: Riboflavin biosynthesis]]
| + | |
| Structural highlights
Function
RIBB_METJA Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.[1]
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
Skeletal rearrangements of carbohydrates are crucial for many biosynthetic pathways. In riboflavin biosynthesis ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions. Here, we present the crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal center presumably consisting of non-catalytic zinc and calcium ions at 1.7-A resolution. The carbonyl group (O2) and two out of three free hydroxyl groups (OH3 and OH4) of the substrate are metal-coordinated. We correlate previous mutational studies on this enzyme with the present structural results. Residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity. Only Glu-185 of the second coordination sphere cannot be replaced without complete loss of activity. It contacts the C3 hydrogen atom directly and probably initiates enediol formation in concert with both metal ions to start the reaction sequence. Mechanistic similarities to Rubisco acting on the similar substrate ribulose 1,5-diphosphate in carbon dioxide fixation as well as other carbohydrate (reducto-) isomerases are discussed.
Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.,Steinbacher S, Schiffmann S, Richter G, Huber R, Bacher A, Fischer M J Biol Chem. 2003 Oct 24;278(43):42256-65. Epub 2003 Aug 6. PMID:12904291[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Fischer M, Romisch W, Schiffmann S, Kelly M, Oschkinat H, Steinbacher S, Huber R, Eisenreich W, Richter G, Bacher A. Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii. J Biol Chem. 2002 Nov 1;277(44):41410-6. Epub 2002 Aug 27. PMID:12200440 doi:http://dx.doi.org/10.1074/jbc.M206863200
- ↑ Steinbacher S, Schiffmann S, Richter G, Huber R, Bacher A, Fischer M. Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism. J Biol Chem. 2003 Oct 24;278(43):42256-65. Epub 2003 Aug 6. PMID:12904291 doi:http://dx.doi.org/10.1074/jbc.M307301200
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