2V81

Native KDPGal structure

Summary for 2V81

• Entry DOI: 10.2210/pdb2v81/pdb
• Related: 2J6N 2J6Q 2V82
• Descriptor: 2-DEHYDRO-3-DEOXY-6-PHOSPHOGALACTONATE ALDOLASE (2 entities in total)
• Functional Keywords: lyase, kdpgal, aldolase
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 1
• Total formula weight: 22489.22

Authors

Naismith, J.H. (deposition date: 2007-08-02, release date: 2007-08-14, Last modification date: 2024-10-16)

Primary citation

Walters, M.J.,Srikannathasan, V.,McEwan, A.R.,Naismith, J.H.,Fierke, C.A.,Toone, E.J.
Characterization and crystal structure of Escherichia coli KDPGal aldolase.
Bioorg. Med. Chem., 16:710-720, 2008

PubMed Abstract: 2-Keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-3-deoxy-6-phosphogalactonate (KDPGal) aldolases catalyze an identical reaction differing in substrate specificity in only the configuration of a single stereocenter. However, the proteins show little sequence homology at the amino acid level. Here we investigate the determinants of substrate selectivity of these enzymes. The Escherichia coli KDPGal aldolase gene, cloned into a T7 expression vector and overexpressed in E. coli, catalyzes retro-aldol cleavage of the natural substrate, KDPGal, with values of k(cat)/K(M) and k(cat) of 1.9x10(4)M(-1)s(-1) and 4s(-1), respectively. In the synthetic direction, KDPGal aldolase efficiently catalyzes an aldol addition using a limited number of aldehyde substrates, including d-glyceraldehyde-3-phosphate (natural substrate), d-glyceraldehyde, glycolaldehyde, and 2-pyridinecarboxaldehyde. A preparative scale reaction between 2-pyridinecarboxaldehyde and pyruvate catalyzed by KDPGal aldolase produced the aldol adduct of the R stereochemistry in >99.7% ee, a result complementary to that observed using the related KDPG aldolase. The native crystal structure has been solved to a resolution of 2.4A and displays the same (alpha/beta)(8) topology, as KDPG aldolase. We have also determined a 2.1A structure of a Schiff base complex between the enzyme and its substrate. This model predicts that a single amino acid change, T161 in KDPG aldolase to V154 in KDPGal aldolase, plays an important role in determining the stereochemical course of enzyme catalysis and this prediction was borne out by site-directed mutagenesis studies. However, additional changes in the enzyme sequence are required to prepare an enzyme with both high catalytic efficiency and altered stereochemistry.

PubMed: 17981470
DOI: 10.1016/j.bmc.2007.10.043

Experimental method

X-RAY DIFFRACTION (2.4 Å)