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[[Image:2nuy.gif|left|200px]]<br /><applet load="2nuy" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2nuy, resolution 2.500&Aring;" />
'''2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate'''<br />


==Overview==
==2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate==
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.
<StructureSection load='2nuy' size='340' side='right'caption='[[2nuy]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2nuy]] 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=2NUY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NUY FirstGlance]. <br>
</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>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></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=2nuy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nuy OCA], [https://pdbe.org/2nuy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nuy RCSB], [https://www.ebi.ac.uk/pdbsum/2nuy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nuy ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nu/2nuy_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2nuy ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2NUY 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> and <scene name='pdbligand=PYR:'>PYR</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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=2NUY OCA].
*[[Aldolase 3D structures|Aldolase 3D structures]]
 
== References ==
==Reference==
<references/>
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]
__TOC__
[[Category: 2-dehydro-3-deoxy-phosphogluconate aldolase]]
</StructureSection>
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Sulfolobus acidocaldarius]]
[[Category: Sulfolobus acidocaldarius DSM 639]]
[[Category: Dijkstra, B W.]]
[[Category: Dijkstra BW]]
[[Category: Eerde, A van.]]
[[Category: Van Eerde A]]
[[Category: MG]]
[[Category: PYR]]
[[Category: tim barrel]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:11:16 2008''

Latest revision as of 09:28, 3 April 2024

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate

Structural highlights

2nuy is a 2 chain structure with sequence from Sulfolobus acidocaldarius DSM 639. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Wolterink-van Loo S, van Eerde A, Siemerink MA, Akerboom J, Dijkstra BW, van der Oost J. Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem J. 2007 May 1;403(3):421-30. PMID:17176250 doi:10.1042/BJ20061419

2nuy, resolution 2.50Å

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