8PO5

Lactobacillus plantarum LpdD

Summary for 8PO5

• Entry DOI: 10.2210/pdb8po5/pdb
• Descriptor: Protein LpdD, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: ubid, ubix, lpdd, flavoprotein
• Biological source: Lactobacillus
• Total number of polymer chains: 2
• Total formula weight: 31859.61

Authors

Gahloth, D.,Leys, D. (deposition date: 2023-07-03, release date: 2024-01-17, Last modification date: 2025-01-29)

Primary citation

Gahloth, D.,Fisher, K.,Marshall, S.,Leys, D.
The prFMNH 2 -binding chaperone LpdD assists UbiD decarboxylase activation.
J.Biol.Chem., 300:105653-105653, 2024

PubMed Abstract: The UbiD enzyme family of prenylated flavin (prFMN)-dependent reversible decarboxylases is near ubiquitously present in microbes. For some UbiD family members, enzyme activation through prFMNH binding and subsequent oxidative maturation of the cofactor readily occurs, both in vivo in a heterologous host and through in vitro reconstitution. However, isolation of the active holo-enzyme has proven intractable for others, notably the canonical Escherichia coli UbiD. We show that E. coli heterologous expression of the small protein LpdD-associated with the UbiD-like gallate decarboxylase LpdC from Lactobacillus plantarum-unexpectedly leads to 3,4-dihydroxybenzoic acid decarboxylation whole-cell activity. This activity was shown to be linked to endogenous E. coli ubiD expression levels. The crystal structure of the purified LpdD reveals a dimeric protein with structural similarity to the eukaryotic heterodimeric proteasome assembly chaperone Pba3/4. Solution studies demonstrate that LpdD protein specifically binds to reduced prFMN species only. The addition of the LpdD-prFMNH complex supports reconstitution and activation of the purified E. coli apo-UbiD in vitro, leading to modest 3,4-dihydroxybenzoic acid decarboxylation. These observations suggest that LpdD acts as a prFMNH-binding chaperone, enabling apo-UbiD activation through enhanced prFMNH incorporation and subsequent oxidative maturation. Hence, while a single highly conserved flavin prenyltransferase UbiX is found associated with UbiD enzymes, our observations suggest considerable diversity in UbiD maturation, ranging from robust autocatalytic to chaperone-mediated processes. Unlocking the full (de)carboxylation scope of the UbiD-enzyme family will thus require more than UbiX coexpression.

PubMed: 38224946
DOI: 10.1016/j.jbc.2024.105653

Experimental method

X-RAY DIFFRACTION (2.1 Å)