6GZO

Crystal structure of NadR protein in complex with NAD and AMP-PNP

Summary for 6GZO

• Entry DOI: 10.2210/pdb6gzo/pdb
• Related: 6GYE 6GYF
• Descriptor: Nicotinamide-nucleotide adenylyltransferase NadR family / Ribosylnicotinamide kinase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: vitamin transport, phosphorylation, nad+, nadr, transport protein
• Biological source: Lactococcus lactis subsp. cremoris (Streptococcus cremoris)
• Total number of polymer chains: 2
• Total formula weight: 90670.56

Authors

Singh, R.,Stetsenko, A.,Jaehme, M.,Guskov, A.,Slotboom, D.J. (deposition date: 2018-07-04, release date: 2019-07-17, Last modification date: 2024-01-17)

Primary citation

Stetsenko, A.,Singh, R.,Jaehme, M.,Guskov, A.,Slotboom, D.J.
Structural and Functional Characterization of NadR fromLactococcus lactis.
Molecules, 25:-, 2020

PubMed Abstract: NadR is a bifunctional enzyme that converts nicotinamide riboside (NR) into nicotinamide mononucleotide (NMN), which is then converted into nicotinamide adenine dinucleotide (NAD). Although a crystal structure of the enzyme from the Gram-negative bacterium is known, structural understanding of its catalytic mechanism remains unclear. Here, we purified the NadR enzyme from and established an assay to determine the combined activity of this bifunctional enzyme. The conversion of NR into NAD showed hyperbolic dependence on the NR concentration, but sigmoidal dependence on the ATP concentration. The apparent cooperativity for ATP may be explained because both reactions catalyzed by the bifunctional enzyme (phosphorylation of NR and adenylation of NMN) require ATP. The conversion of NMN into NAD followed simple Michaelis-Menten kinetics for NMN, but again with the sigmoidal dependence on the ATP concentration. In this case, the apparent cooperativity is unexpected since only a single ATP is used in the NMN adenylyltransferase catalyzed reaction. To determine the possible structural determinants of such cooperativity, we solved the crystal structure of NadR from (NadR). Co-crystallization with NAD, NR, NMN, ATP, and AMP-PNP revealed a 'sink' for adenine nucleotides in a location between two domains. This sink could be a regulatory site, or it may facilitate the channeling of substrates between the two domains.

PubMed: 32331317
DOI: 10.3390/molecules25081940

Experimental method

X-RAY DIFFRACTION (3 Å)