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2oek

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[[Image:2oek.gif|left|200px]]<br /><applet load="2oek" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2oek, resolution 1.80&Aring;" />
 
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'''Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ ions'''<br />
 
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==Overview==
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==Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ ions==
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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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<StructureSection load='2oek' size='340' side='right'caption='[[2oek]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[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>
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==About this Structure==
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==See Also==
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2OEK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEK OCA].
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*[[Enolase 3D structures|Enolase 3D structures]]
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== References ==
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==Reference==
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<references/>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17352497 17352497]
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__TOC__
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</StructureSection>
[[Category: Geobacillus kaustophilus]]
[[Category: Geobacillus kaustophilus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Almo, S.C.]]
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[[Category: Almo SC]]
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[[Category: Fedorov, A.A.]]
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[[Category: Fedorov AA]]
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[[Category: Fedorov, E.V.]]
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[[Category: Fedorov EV]]
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[[Category: Gerlt, J.A.]]
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[[Category: Gerlt JA]]
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[[Category: Imker, H.J.]]
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[[Category: Imker HJ]]
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[[Category: MG]]
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[[Category: "enolase"]]
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[[Category: rubisco-like protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:32:08 2008''
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Current revision

Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ ions

PDB ID 2oek

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