2NUX

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

Summary for 2NUX

• Entry DOI: 10.2210/pdb2nux/pdb
• Related: 1NUY 2NUW
• Descriptor: 2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase, MAGNESIUM ION (3 entities in total)
• Functional Keywords: tim barrel, lyase
• Biological source: Sulfolobus acidocaldarius DSM 639
• Total number of polymer chains: 2
• Total formula weight: 65133.27

Authors

van Eerde, A.,Dijkstra, B.W. (deposition date: 2006-11-10, release date: 2007-04-10, Last modification date: 2023-10-25)

Primary citation

Wolterink-van Loo, S.,van Eerde, A.,Siemerink, M.A.J.,Akerboom, J.,Dijkstra, B.W.,van der Oost, J.
Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases
Biochem.J., 403:421-430, 2007

PubMed Abstract: 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.

PubMed: 17176250
DOI: 10.1042/BJ20061419

Experimental method

X-RAY DIFFRACTION (2.5 Å)