9DH0

The Cryo-EM structure of recombinantly expressed hUGDH in complex with UDP-4-keto-xylose

This is a non-PDB format compatible entry.

Summary for 9DH0

• Entry DOI: 10.2210/pdb9dh0/pdb
• Related: 9DGZ
• EMDB information: 46854
• Descriptor: UDP-glucose 6-dehydrogenase, (2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name) (3 entities in total)
• Functional Keywords: human udp-glucose dehydrogenase, udp-4-keto-xylose, oxidoreductase, oxidoreductase-inhibitor complex, oxidoreductase/inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 6
• Total formula weight: 332700.67

Authors

Kadirvelraj, R.,Walsh Jr, R.M.,Wood, Z.W. (deposition date: 2024-09-03, release date: 2025-03-05, Last modification date: 2025-03-12)

Primary citation

O'Brien, J.H.,Kadirvelraj, R.,Tseng, P.S.,Ross-Kemppinen, N.,Crich, D.,Walsh Jr., R.M.,Wood, Z.A.
Cryo-EM Structure of Recombinantly Expressed hUGDH Unveils a Hidden, Alternative Allosteric Inhibitor.
Biochemistry, 64:92-104, 2025

PubMed Abstract: Human UDP-glucose dehydrogenase (hUGDH) catalyzes the oxidation of UDP-glucose into UDP-glucuronic acid, an essential substrate in the Phase II metabolism of drugs. hUGDH is a hexamer that exists in an equilibrium between an active (E) state and an inactive (E) state, with the latter being stabilized by the binding of the allosteric inhibitor UDP-xylose (UDP-Xyl). The allosteric transition between E and E is slow and can be observed as a lag in progress curves. Previous analysis of the lag suggested that unliganded hUGDH exists mainly as E, but two unique crystal forms suggest that the enzyme favors the E state. Resolving this discrepancy is necessary to fully understand the allosteric mechanism of hUGDH. Here, we used cryo-EM to show that recombinant hUGDH expressed in copurifies with UDP-4-keto-xylose (UX4O), which mimics the UDP-Xyl inhibitor and favors the E state. Cryo-EM studies show that removing UX4O from hUGDH shifts the ensemble to favor the E state. This shift is consistent with progress curve analysis, which shows the absence of a lag for unliganded hUGDH. Inhibition studies show that hUGDH has similar affinities for UDP-Xyl and UX4O. The discovery that UX4O inhibits allosteric hUGDH suggests that UX4O may be the physiologically relevant inhibitor of allosteric UGDHs in bacteria that do not make UDP-Xyl.

PubMed: 39680853
DOI: 10.1021/acs.biochem.4c00555

Experimental method

ELECTRON MICROSCOPY (2.38 Å)