7YQP

Xcc Nicotinamide Phosphoribosyltransferase

Summary for 7YQP

• Entry DOI: 10.2210/pdb7yqp/pdb
• Descriptor: Pre-B cell enhancing factor related protein (2 entities in total)
• Functional Keywords: nampt in isolation, transferase
• Biological source: Xanthomonas campestris pv. campestris
• Total number of polymer chains: 1
• Total formula weight: 53213.75

Authors

Xu, G.L.,Ming, Z.H. (deposition date: 2022-08-08, release date: 2024-02-14, Last modification date: 2024-09-04)

Primary citation

Xu, G.,Ma, J.,Fang, Q.,Peng, Q.,Jiao, X.,Hu, W.,Zhao, Q.,Kong, Y.,Liu, F.,Shi, X.,Tang, D.J.,Tang, J.L.,Ming, Z.
Structural insights into Xanthomonas campestris pv. campestris NAD + biosynthesis via the NAM salvage pathway.
Commun Biol, 7:255-255, 2024

PubMed Abstract: Nicotinamide phosphoribosyltransferase (NAMPT) plays an important role in the biosynthesis of nicotinamide adenine dinucleotide (NAD) via the nicotinamide (NAM) salvage pathway. While the structural biochemistry of eukaryote NAMPT has been well studied, the catalysis mechanism of prokaryote NAMPT at the molecular level remains largely unclear. Here, we demonstrated the NAMPT-mediated salvage pathway is functional in the Gram-negative phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc) for the synthesis of NAD, and the enzyme activity of NAMPT in this bacterium is significantly higher than that of human NAMPT in vitro. Our structural analyses of Xcc NAMPT, both in isolation and in complex with either the substrate NAM or the product nicotinamide mononucleotide (NMN), uncovered significant details of substrate recognition. Specifically, we revealed the presence of a NAM binding tunnel that connects the active site, and this tunnel is essential for both catalysis and inhibitor binding. We further demonstrated that NAM binding in the tunnel has a positive cooperative effect with NAM binding in the catalytic site. Additionally, we discovered that phosphorylation of the His residue at position 229 enhances the substrate binding affinity of Xcc NAMPT and is important for its catalytic activity. This work reveals the importance of NAMPT in bacterial NAD synthesis and provides insights into the substrate recognition and the catalytic mechanism of bacterial type II phosphoribosyltransferases.

PubMed: 38429435
DOI: 10.1038/s42003-024-05921-3

Experimental method

X-RAY DIFFRACTION (2.088 Å)