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| ==Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ ions== | | ==Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ ions== |
| <StructureSection load='2oek' size='340' side='right' caption='[[2oek]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='2oek' size='340' side='right'caption='[[2oek]], [[Resolution|resolution]] 1.80Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[2oek]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OEK FirstGlance]. <br> | | <table><tr><td colspan='2'>[[2oek]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OEK FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.8Å</td></tr> |
| <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2oej|2oej]], [[2oel|2oel]], [[2oem|2oem]]</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=2oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oek OCA], [https://pdbe.org/2oek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oek RCSB], [https://www.ebi.ac.uk/pdbsum/2oek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oek ProSAT]</span></td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mtnW ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</td></tr>
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| <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=2oek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oek OCA], [http://pdbe.org/2oek PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oek RCSB], [http://www.ebi.ac.uk/pdbsum/2oek PDBsum]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/MTNW_GEOKA MTNW_GEOKA]] Catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P).<ref>PMID:17352497</ref> | | [https://www.uniprot.org/uniprot/MTNW_GEOKA MTNW_GEOKA] Catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P).<ref>PMID:17352497</ref> |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| D-Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme, is the paradigm member of the recently recognized mechanistically diverse RuBisCO superfamily. The RuBisCO reaction is initiated by abstraction of the proton from C3 of the d-ribulose 1,5-bisphosphate substrate by a carbamate oxygen of carboxylated Lys 201 (spinach enzyme). Heterofunctional homologues of RuBisCO found in species of Bacilli catalyze the tautomerization ("enolization") of 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P) in the methionine salvage pathway in which 5-methylthio-d-ribose (MTR) derived from 5'-methylthioadenosine is converted to methionine [Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N., and Yokota, A. (2003) A functional link between RuBisCO-like protein of Bacillus and photosynthetic RuBisCO, Science 302, 286-290]. The reaction catalyzed by this "enolase" is accomplished by abstraction of a proton from C1 of the DK-MTP 1-P substrate to form the tautomerized product, a conjugated enol. Because the RuBisCO- and "enolase"-catalyzed reactions differ in the regiochemistry of proton abstraction but are expected to share stabilization of an enolate anion intermediate by coordination to an active site Mg2+, we sought to establish structure-function relationships for the "enolase" reaction so that the structural basis for the functional diversity could be established. We determined the stereochemical course of the reaction catalyzed by the "enolases" from Bacillus subtilis and Geobacillus kaustophilus. Using stereospecifically deuterated samples of an alternate substrate derived from d-ribose (5-OH group instead of the 5-methylthio group in MTR) as well as of the natural DK-MTP 1-P substrate, we determined that the "enolase"-catalyzed reaction involves abstraction of the 1-proS proton. We also determined the structure of the activated "enolase" from G. kaustophilus (carboxylated on Lys 173) liganded with Mg2+ and 2,3-diketohexane 1-phosphate, a stable alternate substrate. The stereospecificity of proton abstraction restricts the location of the general base to the N-terminal alpha+beta domain instead of the C-terminal (beta/alpha)8-barrel domain that contains the carboxylated Lys 173. Lys 98 in the N-terminal domain, conserved in all "enolases", is positioned to abstract the 1-proS proton. Consistent with this proposed function, the K98A mutant of the G. kaustophilus "enolase" is unable to catalyze the "enolase" reaction. Thus, we conclude that this functionally divergent member of the RuBisCO superfamily uses the same structural strategy as RuBisCO for stabilizing the enolate anion intermediate, i.e., coordination to an essential Mg2+, but the proton abstraction is catalyzed by a different general base.
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| Mechanistic diversity in the RuBisCO superfamily: the "enolase" in the methionine salvage pathway in Geobacillus kaustophilus.,Imker HJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA Biochemistry. 2007 Apr 3;46(13):4077-89. Epub 2007 Mar 13. PMID:17352497<ref>PMID:17352497</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 2oek" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[Enolase|Enolase]] | | *[[Enolase 3D structures|Enolase 3D structures]] |
| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Bacillus kaustophilus prickett 1928]] | | [[Category: Geobacillus kaustophilus]] |
| [[Category: Almo, S C]] | | [[Category: Large Structures]] |
| [[Category: Fedorov, A A]] | | [[Category: Almo SC]] |
| [[Category: Fedorov, E V]] | | [[Category: Fedorov AA]] |
| [[Category: Gerlt, J A]] | | [[Category: Fedorov EV]] |
| [[Category: Imker, H J]] | | [[Category: Gerlt JA]] |
| [[Category: Enolase]] | | [[Category: Imker HJ]] |
| [[Category: Isomerase]]
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| [[Category: Rubisco-like protein]]
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