PDBsum entry: 2nux

Lyase

PDB id: 2nux

Contents

Protein chains

288 a.a. *

Metals

_MG

Waters ×94

* Residue conservation analysis

PDB id:

2nux

Name:

Lyase

Title:

2-keto-3-deoxygluconate aldolase from sulfolobus acidocaldar native structure in p6522 at 2.5 a resolution

Structure:

2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho aldolase. Chain: a, b. Engineered: yes

Source:

Sulfolobus acidocaldarius dsm 639. Organism_taxid: 330779. Strain: dsm639. Gene: saci_0225. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.50Å R-factor: 0.177 R-free: 0.216

Authors:

A.Van Eerde,B.W.Dijkstra

Key ref:

S.Wolterink-van Loo et al. (2007). Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem J, 403, 421-430. PubMed id: 17176250 DOI: 10.1042/BJ20061419

Date:

10-Nov-06 Release date: 10-Apr-07

Protein chains

Q4JC35  (Q4JC35_SULAC) -  2-keto-3-deoxygluconate/2-keto-3-deoxy-6-phospho gluconate aldolase

Seq: 288 a.a.

Struc: 288 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: metabolic process (1 term)
• Biochemical function: catalytic activity (2 terms)

DOI no: 10.1042/BJ20061419

Biochem J 403:421-430 (2007)

PubMed id: 17176250

Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases.

S.Wolterink-van Loo, A.van Eerde, M.A.Siemerink, J.Akerboom, B.W.Dijkstra, J.van der Oost.

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.