6ZLD

Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Glucuronic acid and NAD

Summary for 6ZLD

• Entry DOI: 10.2210/pdb6zld/pdb
• Descriptor: Epimerase domain-containing protein, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID, ... (4 entities in total)
• Functional Keywords: epimerase, udp-glucuronic acid, nad, oxidoreductase, udp-sugar binding protein
• Biological source: Bacillus cereus HuA2-4
• Total number of polymer chains: 2
• Total formula weight: 75541.33

Authors

Iacovino, L.G.,Savino, S.,Mattevi, A. (deposition date: 2020-06-30, release date: 2020-07-29, Last modification date: 2024-01-31)

Primary citation

Iacovino, L.G.,Savino, S.,Borg, A.J.E.,Binda, C.,Nidetzky, B.,Mattevi, A.
Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction.
J.Biol.Chem., 295:12461-12473, 2020

PubMed Abstract: UDP-glucuronic acid is converted to UDP-galacturonic acid en route to a variety of sugar-containing metabolites. This reaction is performed by a NAD-dependent epimerase belonging to the short-chain dehydrogenase/reductase family. We present several high-resolution crystal structures of the UDP-glucuronic acid epimerase from The geometry of the substrate-NAD interactions is finely arranged to promote hydride transfer. The exquisite complementarity between glucuronic acid and its binding site is highlighted by the observation that the unligated cavity is occupied by a cluster of ordered waters whose positions overlap the polar groups of the sugar substrate. Co-crystallization experiments led to a structure where substrate- and product-bound enzymes coexist within the same crystal. This equilibrium structure reveals the basis for a "swing and flip" rotation of the pro-chiral 4-keto-hexose-uronic acid intermediate that results from glucuronic acid oxidation, placing the C4' atom in position for receiving a hydride ion on the opposite side of the sugar ring. The product-bound active site is almost identical to that of the substrate-bound structure and satisfies all hydrogen-bonding requirements of the ligand. The structure of the apoenzyme together with the kinetic isotope effect and mutagenesis experiments further outlines a few flexible loops that exist in discrete conformations, imparting structural malleability required for ligand rotation while avoiding leakage of the catalytic intermediate and/or side reactions. These data highlight the double nature of the enzymatic mechanism: the active site features a high degree of precision in substrate recognition combined with the flexibility required for intermediate rotation.

PubMed: 32661196
DOI: 10.1074/jbc.RA120.014692

Experimental method

X-RAY DIFFRACTION (1.8 Å)