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Literature summary extracted from

  • 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 (2015), Proc. Natl. Acad. Sci. USA, 112, 13348-13353.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.7.6.5 gene yjbM, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Bacillus subtilis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.6.5 purified enzyme in presence of ATP and GTP, 1 week, X-ray diffraction structure determination and analysis at 2.94 A resolution Bacillus subtilis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.7.6.5 additional information
-
 additional information alarmone synthesis in SAS1 proceeds in a highly cooperative manner Bacillus subtilis
2.7.6.5 1.2
-
 GDP pH 7.5, 37°C, recombinant enzyme Bacillus subtilis
2.7.6.5 1.7
-
 GTP pH 7.5, 37°C, recombinant enzyme Bacillus subtilis
2.7.6.5 2
-
 guanosine 3'-diphosphate 5'-triphosphate pH 7.5, 37°C, recombinant enzyme Bacillus subtilis
2.7.6.5 3
-
 guanosine 3'-diphosphate 5'-diphosphate pH 7.5, 37°C, recombinant enzyme Bacillus subtilis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.6.5 Mg2+ required, binding structure analysis, overview Bacillus subtilis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.6.5 ATP + GDP Bacillus subtilis
-
 AMP + guanosine 3'-diphosphate 5'-diphosphate
-
 ?
2.7.6.5 ATP + GDP Bacillus subtilis 168
-
 AMP + guanosine 3'-diphosphate 5'-diphosphate
-
 ?
2.7.6.5 ATP + GTP Bacillus subtilis
-
 AMP + guanosine 3'-diphosphate 5'-triphosphate
-
 ?
2.7.6.5 ATP + GTP Bacillus subtilis 168
-
 AMP + guanosine 3'-diphosphate 5'-triphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-diphosphate + H2O Bacillus subtilis
-
 GDP + diphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-diphosphate + H2O Bacillus subtilis 168
-
 GDP + diphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-triphosphate + H2O Bacillus subtilis
-
 GTP + diphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-triphosphate + H2O Bacillus subtilis 168
-
 GTP + diphosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.6.5 Bacillus subtilis O31611 gene yjbM
-
2.7.6.5 Bacillus subtilis 168 O31611 gene yjbM
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.7.6.5 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration Bacillus subtilis

Reaction

EC Number Reaction Comment Organism Reaction ID
2.7.6.5 ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate the catalytic pathway of (p)ppGpp synthesis involves a sequentially ordered substrate binding, activation of ATP in a strained conformation, and transfer of diphosphate through a nucleophilic substitution (SN2) reaction. pppGpp, but not ppGpp, positively regulates the enzyme at an allosteric site Bacillus subtilis
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.6.5 ATP + GDP
-
 Bacillus subtilis AMP + guanosine 3'-diphosphate 5'-diphosphate
-
 ?
2.7.6.5 ATP + GDP
-
 Bacillus subtilis 168 AMP + guanosine 3'-diphosphate 5'-diphosphate
-
 ?
2.7.6.5 ATP + GTP
-
 Bacillus subtilis AMP + guanosine 3'-diphosphate 5'-triphosphate
-
 ?
2.7.6.5 ATP + GTP
-
 Bacillus subtilis 168 AMP + guanosine 3'-diphosphate 5'-triphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-diphosphate + H2O
-
 Bacillus subtilis GDP + diphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-diphosphate + H2O
-
 Bacillus subtilis 168 GDP + diphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-triphosphate + H2O
-
 Bacillus subtilis GTP + diphosphate
-
 ?
2.7.6.5 guanosine 3'-diphosphate 5'-triphosphate + H2O
-
 Bacillus subtilis 168 GTP + diphosphate
-
 ?
2.7.6.5 additional information the enzyme is bifunctional showing synthase activity forming ppGpp and pppGpp, and hydrolase activity with the two compounds resulting in formation of GTP or GDP and diphosphate Bacillus subtilis ?
-
 ?
2.7.6.5 additional information the enzyme is bifunctional showing synthase activity forming ppGpp and pppGpp, and hydrolase activity with the two compounds resulting in formation of GTP or GDP and diphosphate Bacillus subtilis 168 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
2.7.6.5 homotetramer domain structure and three-dimensional homology modelling, sequence comparisons, crystal structure analysis, overview Bacillus subtilis

Synonyms

EC Number Synonyms Comment Organism
2.7.6.5 (p)ppGpp synthetase
-
 Bacillus subtilis
2.7.6.5 alarmone synthetase
-
 Bacillus subtilis
2.7.6.5 SAS1
-
 Bacillus subtilis
2.7.6.5 small alarmone synthetase 1
-
 Bacillus subtilis
2.7.6.5 YjbM
-
 Bacillus subtilis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.7.6.5 37
-
 assay at Bacillus subtilis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.7.6.5 7.5
-
 assay at Bacillus subtilis

Cofactor

EC Number Cofactor Comment Organism Structure
2.7.6.5 ATP binding structure analysis, overview Bacillus subtilis

General Information

EC Number General Information Comment Organism
2.7.6.5 evolution the enzyme belongs to the RSH superfamily, which controls concentrations of the alarmones (p)ppGpp (guanosine penta- or tetra-phosphate) Bacillus subtilis
2.7.6.5 additional information mechanism and allosteric regulation of the highly cooperative enzyme from Bacillus subtilis, overview. Analysis of the catalytic mechanism of (p)ppGpp synthesis by oligomeric and highly cooperative small alarmone synthetase 1 (SAS1) at atomic resolution, structural and biochemical analysis reveals that only pppGpp, but not ppGpp, positively affects the activity of the enzyme Bacillus subtilis
2.7.6.5 physiological function guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively termed (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 diphosphate from ATP to GDP or GTP. ppGpp and pppGpp execute different functional roles Bacillus subtilis