2nux

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(New page: 200px<br /><applet load="2nux" size="350" color="white" frame="true" align="right" spinBox="true" caption="2nux, resolution 2.500&Aring;" /> '''2-keto-3-deoxygluco...)
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[[Image:2nux.gif|left|200px]]<br /><applet load="2nux" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2nux, resolution 2.500&Aring;" />
 
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'''2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure in p6522 at 2.5 A resolution'''<br />
 
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==Overview==
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==2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure in p6522 at 2.5 A resolution==
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Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present, study, the genomes of Sulfolobus species were screened for aldolases. Two, new KDGA [2-keto-3-deoxygluconate (2-oxo-3-deoxygluconate) aldolases] from, Sulfolobus acidocaldarius and Sulfolobus tokodaii were identified, overexpressed in Escherichia coli and characterized. Both enzymes were, found to have biochemical properties similar to the previously, characterized S. solfataricus KDGA, including the condensation of pyruvate, and either D,L-glyceraldehyde or D,L-glyceraldehyde 3-phosphate. The, crystal structure of S. acidocaldarius KDGA revealed the presence of a, novel phosphate-binding motif that allows the formation of multiple, hydrogen-bonding interactions with the acceptor substrate, and enables, high activity with glyceraldehyde 3-phosphate. Activity analyses with, unnatural substrates revealed that these three KDGAs readily accept, aldehydes with two to four carbon atoms, and that even aldoses with five, carbon atoms are accepted to some extent. Water-mediated interactions, permit binding of substrates in multiple conformations in the spacious, hydrophilic binding site, and correlate with the observed broad substrate, specificity.
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<StructureSection load='2nux' size='340' side='right'caption='[[2nux]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2nux]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius_DSM_639 Sulfolobus acidocaldarius DSM 639]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NUX 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]] 2.5&#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=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=2nux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nux OCA], [https://pdbe.org/2nux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nux RCSB], [https://www.ebi.ac.uk/pdbsum/2nux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nux ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/KDGA_SULAC KDGA_SULAC] Involved in the degradation of glucose and galactose via the Entner-Doudoroff pathway. Catalyzes the reversible cleavage of 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxygluconate (KDG) forming pyruvate and glyceraldehyde 3-phosphate or glyceraldehyde, respectively. It is also able to catalyze the reversible cleavage of 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) and 2-keto-3-deoxygalactonate (KDGal).<ref>PMID:17176250</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nu/2nux_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2nux ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Aldolases are enzymes with potential applications in biosynthesis, depending on their activity, specificity and stability. In the present study, the genomes of Sulfolobus species were screened for aldolases. Two new KDGA [2-keto-3-deoxygluconate (2-oxo-3-deoxygluconate) aldolases] from Sulfolobus acidocaldarius and Sulfolobus tokodaii were identified, overexpressed in Escherichia coli and characterized. Both enzymes were found to have biochemical properties similar to the previously characterized S. solfataricus KDGA, including the condensation of pyruvate and either D,L-glyceraldehyde or D,L-glyceraldehyde 3-phosphate. The crystal structure of S. acidocaldarius KDGA revealed the presence of a novel phosphate-binding motif that allows the formation of multiple hydrogen-bonding interactions with the acceptor substrate, and enables high activity with glyceraldehyde 3-phosphate. Activity analyses with unnatural substrates revealed that these three KDGAs readily accept aldehydes with two to four carbon atoms, and that even aldoses with five carbon atoms are accepted to some extent. Water-mediated interactions permit binding of substrates in multiple conformations in the spacious hydrophilic binding site, and correlate with the observed broad substrate specificity.
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==About this Structure==
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Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases.,Wolterink-van Loo S, van Eerde A, Siemerink MA, Akerboom J, Dijkstra BW, van der Oost J Biochem J. 2007 May 1;403(3):421-30. PMID:17176250<ref>PMID:17176250</ref>
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2NUX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_acidocaldarius Sulfolobus acidocaldarius] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/2-dehydro-3-deoxy-phosphogluconate_aldolase 2-dehydro-3-deoxy-phosphogluconate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.14 4.1.2.14] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NUX OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases., Wolterink-van Loo S, van Eerde A, Siemerink MA, Akerboom J, Dijkstra BW, van der Oost J, Biochem J. 2007 May 1;403(3):421-30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17176250 17176250]
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</div>
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[[Category: 2-dehydro-3-deoxy-phosphogluconate aldolase]]
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<div class="pdbe-citations 2nux" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Sulfolobus acidocaldarius]]
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[[Category: Dijkstra, B.W.]]
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[[Category: Eerde, A.van.]]
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[[Category: MG]]
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[[Category: tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 20:59:51 2008''
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==See Also==
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*[[Aldolase 3D structures|Aldolase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Sulfolobus acidocaldarius DSM 639]]
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[[Category: Dijkstra BW]]
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[[Category: Van Eerde A]]

Current revision

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure in p6522 at 2.5 A resolution

PDB ID 2nux

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