5DED

Crystal structure of the small alarmone synthethase 1 from Bacillus subtilis bound to its product pppGpp

Summary for 5DED

• Entry DOI: 10.2210/pdb5ded/pdb
• Descriptor: GTP pyrophosphokinase YjbM, guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate), MAGNESIUM ION (3 entities in total)
• Functional Keywords: (p)ppgpp, alarmone, stringent response, allosteric regulator, transferase
• Biological source: Bacillus subtilis PY79
• Total number of polymer chains: 8
• Total formula weight: 213329.32

Authors

Steinchen, W.,Schuhmacher, J.S.,Altegoer, F.,Bange, G. (deposition date: 2015-08-25, release date: 2015-10-28, Last modification date: 2024-01-10)

Primary citation

Steinchen, W.,Schuhmacher, J.S.,Altegoer, F.,Fage, C.D.,Srinivasan, V.,Linne, U.,Marahiel, M.A.,Bange, G.
Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp synthetase by an alarmone.
Proc.Natl.Acad.Sci.USA, 112:13348-13353, 2015

PubMed Abstract: Nucleotide-based second messengers serve in the response of living organisms to environmental changes. In bacteria and plant chloroplasts, guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) [collectively named "(p)ppGpp"] act as alarmones that globally reprogram cellular physiology during various stress conditions. Enzymes of the RelA/SpoT homology (RSH) family synthesize (p)ppGpp by transferring pyrophosphate from ATP to GDP or GTP. Little is known about the catalytic mechanism and regulation of alarmone synthesis. It also is unclear whether ppGpp and pppGpp execute different functions. Here, we unravel the mechanism and allosteric regulation of the highly cooperative alarmone synthetase small alarmone synthetase 1 (SAS1) from Bacillus subtilis. We determine that the catalytic pathway of (p)ppGpp synthesis involves a sequentially ordered substrate binding, activation of ATP in a strained conformation, and transfer of pyrophosphate through a nucleophilic substitution (SN2) reaction. We show that pppGpp-but not ppGpp-positively regulates SAS1 at an allosteric site. Although the physiological significance remains to be elucidated, we establish the structural and mechanistic basis for a biological activity in which ppGpp and pppGpp execute different functional roles.

PubMed: 26460002
DOI: 10.1073/pnas.1505271112

Experimental method

X-RAY DIFFRACTION (2.942 Å)