2nuw: Difference between revisions

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[[Image:2nuw.png|left|200px]]


{{STRUCTURE_2nuw| PDB=2nuw | SCENE= }}
==2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 A resolution==
<StructureSection load='2nuw' size='340' side='right'caption='[[2nuw]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2nuw]] 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=2NUW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NUW 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]] 1.8&#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></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=2nuw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nuw OCA], [https://pdbe.org/2nuw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nuw RCSB], [https://www.ebi.ac.uk/pdbsum/2nuw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nuw 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/2nuw_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=2nuw ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 A resolution===
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>


{{ABSTRACT_PUBMED_17176250}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 2nuw" style="background-color:#fffaf0;"></div>
[[2nuw]] is a 2 chain structure of [[Aldolase]] with sequence from [http://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=2NUW OCA].


==See Also==
==See Also==
*[[Aldolase|Aldolase]]
*[[Aldolase 3D structures|Aldolase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:017176250</ref><references group="xtra"/>
__TOC__
[[Category: 2-dehydro-3-deoxy-phosphogluconate aldolase]]
</StructureSection>
[[Category: Sulfolobus acidocaldarius dsm 639]]
[[Category: Large Structures]]
[[Category: Dijkstra, B W.]]
[[Category: Sulfolobus acidocaldarius DSM 639]]
[[Category: Eerde, A van.]]
[[Category: Dijkstra BW]]
[[Category: Lyase]]
[[Category: Van Eerde A]]
[[Category: Tim barrel]]

Latest revision as of 11:55, 25 October 2023

2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 A resolution2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 A resolution

Structural highlights

2nuw 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 1.8Å
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.

Publication Abstract from PubMed

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.

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[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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
  2. 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

2nuw, resolution 1.80Å

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