6W1I

Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).

Summary for 6W1I

• Entry DOI: 10.2210/pdb6w1i/pdb
• Related: 6D9Q 6D9R 6D9S
• Descriptor: Xanthine phosphoribosyltransferase, SODIUM ION, GUANOSINE-5',3'-TETRAPHOSPHATE, ... (4 entities in total)
• Functional Keywords: (p)ppgpp, salvage, gtp, homeostasis, xprt, prpp, purine, structural genomics, psi-2, protein structure initiative, midwest center for structural genomics, mcsg, transferase
• Biological source: Bacillus subtilis (strain 168)
• Total number of polymer chains: 4
• Total formula weight: 88504.92

Authors

Satyshur, K.A.,Anderson, B.W.,Keck, J.L.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2020-03-04, release date: 2020-07-29, Last modification date: 2024-10-23)

Primary citation

Anderson, B.W.,Hao, A.,Satyshur, K.A.,Keck, J.L.,Wang, J.D.
Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp.
J.Mol.Biol., 432:4108-4126, 2020

PubMed Abstract: The alarmones pppGpp and ppGpp mediate starvation response and maintain purine homeostasis to protect bacteria. In the bacterial phyla Firmicutes and Bacteroidetes, xanthine phosphoribosyltransferase (XPRT) is a purine salvage enzyme that produces the nucleotide XMP from PRPP and xanthine. Combining structural, biochemical, and genetic analyses, we show that pppGpp and ppGpp, as well as a third newly identified alarmone pGpp, all directly interact with XPRT from the Gram-positive bacterium Bacillus subtilis and inhibit XPRT activity by competing with its substrate PRPP. Structural analysis reveals that ppGpp binds the PRPP binding motif within the XPRT active site. This motif is present in another (p)ppGpp target, the purine salvage enzyme HPRT, suggesting evolutionary conservation in different enzymes. However, XPRT oligomeric interaction is distinct from HPRT in that XPRT forms a symmetric dimer with two (p)ppGpp binding sites at the dimer interface. (p)ppGpp's interaction with an XPRT bridging loop across the interface results in XPRT cooperatively binding (p)ppGpp. Also, XPRT displays differential regulation by the alarmones as it is potently inhibited by both ppGpp and pGpp, but only modestly by pppGpp. Lastly, we demonstrate that the alarmones are necessary for protecting GTP homeostasis against excess environmental xanthine in B. subtilis, suggesting that regulation of XPRT is key for regulating the purine salvage pathway.

PubMed: 32446804
DOI: 10.1016/j.jmb.2020.05.013

Experimental method

X-RAY DIFFRACTION (1.8 Å)