1NAI

UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED

Summary for 1NAI

• Entry DOI: 10.2210/pdb1nai/pdb
• Descriptor: UDP-GALACTOSE 4-EPIMERASE, SODIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (7 entities in total)
• Functional Keywords: isomerase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 38589.80

Authors

Thoden, J.B.,Frey, P.A.,Holden, H.M. (deposition date: 1995-11-22, release date: 1996-12-23, Last modification date: 2024-02-14)

Primary citation

Thoden, J.B.,Frey, P.A.,Holden, H.M.
Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli.
Biochemistry, 35:2557-2566, 1996

PubMed Abstract: UDP-galactose 4-epimerase catalyzes the conversion of UDP-galactose to UDP-glucose through a mechanism involving the transient reduction of NAD+. Here we describe the X-ray structures for epimerase complexed with NADH/UDP, and NAD+/UDP, refined to 1.8 and 2.0 angstrom, respectively. The alpha-carbon positions for the two forms of the enzyme are superimposed with a root-mean-square deviation of 0.36 A. Overall, the models for the reduced and oxidized proteins are very similar except for the positions of several side chains including Phe 178 and Phe 218. The most striking difference between the oxidized and reduced enzymes is the conformation of the nicotinamide ring of the dinucleotide. In the reduced protein, the nicotinamide ring adopts the anti conformation while in the oxidized enzyme the syn conformation is observed. There are also significant structural differences in UDP binding between the oxidized and reduced forms of the protein which most likely explain the observation that uridine nucleotides bind more tightly to epimerase/NADH than to epimerase/NAD+. Both van der Waals and electrostatic interactions between epimerase and NAD+ are extensive with 35 contacts below 3.2 angstrom as would be expected for enzyme that binds the dinucleotide irreversibly. This is in sharp contrast to the patterns typically observed for the NAD+-dependent dehydrogenases which bind nucleotides in a reversible fashion. While it has been postulated that the active site of epimerase must contain a base, the only potential candidates within approximately 5 A of both the NAD+ and the UDP are Asp 31, Asp 58, and ASP 295. These amino acid residues, however, are intimately involved in nucleotide binding and most likely do not play a role in the actual catalytic mechanism. Thus it may be speculated that an amino acid residue, other than glutamate, aspartate, or histidine, may be functioning as the active site base.

PubMed: 8611559
DOI: 10.1021/bi952715y

Experimental method

X-RAY DIFFRACTION (2 Å)