YJBM_BACSU
ID YJBM_BACSU Reviewed; 211 AA.
AC O31611;
DT 19-JAN-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 103.
DE RecName: Full=GTP pyrophosphokinase YjbM;
DE EC=2.7.6.5 {ECO:0000269|PubMed:26460002};
DE AltName: Full=(p)ppGpp synthase YjbM;
DE AltName: Full=Small alarmone synthase 1 {ECO:0000303|PubMed:18067544};
DE Short=SAS 1 {ECO:0000303|PubMed:18067544};
GN Name=yjbM; OrderedLocusNames=BSU11600;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP FUNCTION AS A (P)PPGPP SYNTHASE, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=18067544; DOI=10.1111/j.1365-2958.2007.06018.x;
RA Nanamiya H., Kasai K., Nozawa A., Yun C.S., Narisawa T., Murakami K.,
RA Natori Y., Kawamura F., Tozawa Y.;
RT "Identification and functional analysis of novel (p)ppGpp synthetase genes
RT in Bacillus subtilis.";
RL Mol. Microbiol. 67:291-304(2008).
RN [3]
RP INDUCTION.
RC STRAIN=168;
RX PubMed=22950019; DOI=10.1002/mbo3.16;
RA Tagami K., Nanamiya H., Kazo Y., Maehashi M., Suzuki S., Namba E.,
RA Hoshiya M., Hanai R., Tozawa Y., Morimoto T., Ogasawara N., Kageyama Y.,
RA Ara K., Ozaki K., Yoshida M., Kuroiwa H., Kuroiwa T., Ohashi Y.,
RA Kawamura F.;
RT "Expression of a small (p)ppGpp synthetase, YwaC, in the (p)ppGpp(0) mutant
RT of Bacillus subtilis triggers YvyD-dependent dimerization of ribosome.";
RL MicrobiologyOpen 1:115-134(2012).
RN [4] {ECO:0007744|PDB:5DEC, ECO:0007744|PDB:5DED, ECO:0007744|PDB:5F2V}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 2-211 APO-FORM AND IN COMPLEXES
RP WITH ATP ANALOG OR PPPGPP, FUNCTION, REACTION MECHANISM, CATALYTIC
RP ACTIVITY, ACTIVITY REGULATION, ACTIVE SITE, SUBUNIT, ATP-BINDING, AND
RP MUTAGENESIS OF LYS-25; PHE-42; ARG-46; GLU-139 AND ASN-148.
RC STRAIN=168 / PY79;
RX PubMed=26460002; DOI=10.1073/pnas.1505271112;
RA Steinchen W., Schuhmacher J.S., Altegoer F., Fage C.D., Srinivasan V.,
RA Linne U., Marahiel M.A., Bange G.;
RT "Catalytic mechanism and allosteric regulation of an oligomeric (p)ppGpp
RT synthetase by an alarmone.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:13348-13353(2015).
CC -!- FUNCTION: Functions as a (p)ppGpp synthase; GDP can be used instead of
CC GTP, resulting in an increase of (p)ppGpp synthesis (PubMed:18067544).
CC The enzyme binds ATP, then GDP or GTP and catalysis is highly
CC cooperative (PubMed:26460002). In eubacteria ppGpp (guanosine 3'-
CC diphosphate 5'-diphosphate) is a mediator of the stringent response
CC that coordinates a variety of cellular activities in response to
CC changes in nutritional abundance. Probably has a minor role in the
CC stringent response (PubMed:18067544). {ECO:0000269|PubMed:18067544,
CC ECO:0000269|PubMed:26460002}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate;
CC Xref=Rhea:RHEA:22088, ChEBI:CHEBI:30616, ChEBI:CHEBI:37565,
CC ChEBI:CHEBI:142410, ChEBI:CHEBI:456215; EC=2.7.6.5;
CC Evidence={ECO:0000269|PubMed:26460002};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:22089;
CC Evidence={ECO:0000305|PubMed:26460002};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + GDP = AMP + guanosine 3',5'-bis(diphosphate);
CC Xref=Rhea:RHEA:28098, ChEBI:CHEBI:30616, ChEBI:CHEBI:58189,
CC ChEBI:CHEBI:77828, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:26460002};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:28099;
CC Evidence={ECO:0000305|PubMed:26460002};
CC -!- ACTIVITY REGULATION: Allosterically regulated by its own products;
CC pppGpp simulates synthesis 10-fold more than ppGpp. 2 pppGpp molecules
CC bind in a regulatory cleft in the middle of the tetramer in an
CC asymmetric manner. There is a specific contact of Lys-25 to the gamma-
CC phosphate of pppGpp, explaining why pppGpp stimulates activity but
CC ppGpp does not (PubMed:26460002). {ECO:0000269|PubMed:26460002}.
CC -!- PATHWAY: Purine metabolism; ppGpp biosynthesis; ppGpp from GTP: step
CC 1/2.
CC -!- SUBUNIT: Homotetramer (PubMed:26460002). {ECO:0000269|PubMed:26460002}.
CC -!- INDUCTION: Expressed during exponential growth through the transition
CC to the stationary phase, but not during entry of cells into stationary
CC phase (PubMed:18067544). Protein continuously expressed with a peak at
CC 2 hours after inoculation, decreasing until 3.5 hours as cells enter
CC stationary phase (at protein level) (PubMed:22950019).
CC {ECO:0000269|PubMed:18067544, ECO:0000269|PubMed:22950019}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype, double yjbM-ywaC and triple
CC relA-yjbM-ywaC mutants are also viable (PubMed:18067544).
CC {ECO:0000269|PubMed:18067544}.
CC -!- MISCELLANEOUS: The synthase activity of YjbM is greater than that of
CC YwaC (PubMed:18067544). {ECO:0000269|PubMed:18067544}.
CC -!- SIMILARITY: Belongs to the RelA/SpoT family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AL009126; CAB13017.1; -; Genomic_DNA.
DR PIR; E69844; E69844.
DR RefSeq; NP_389042.1; NC_000964.3.
DR RefSeq; WP_003245294.1; NZ_JNCM01000035.1.
DR PDB; 5DEC; X-ray; 2.00 A; A/B/C/D=2-211.
DR PDB; 5DED; X-ray; 2.94 A; A/B/C/D/E/F/G/H=2-211.
DR PDB; 5F2V; X-ray; 2.80 A; O/P/Q/R/S/T/U/V/W/X/Y/Z=3-211.
DR PDBsum; 5DEC; -.
DR PDBsum; 5DED; -.
DR PDBsum; 5F2V; -.
DR AlphaFoldDB; O31611; -.
DR SMR; O31611; -.
DR STRING; 224308.BSU11600; -.
DR PaxDb; O31611; -.
DR PRIDE; O31611; -.
DR EnsemblBacteria; CAB13017; CAB13017; BSU_11600.
DR GeneID; 939809; -.
DR KEGG; bsu:BSU11600; -.
DR PATRIC; fig|224308.179.peg.1249; -.
DR eggNOG; COG2357; Bacteria.
DR InParanoid; O31611; -.
DR OMA; VWATIEH; -.
DR PhylomeDB; O31611; -.
DR BioCyc; BSUB:BSU11600-MON; -.
DR BRENDA; 2.7.6.5; 658.
DR UniPathway; UPA00908; UER00884.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0008728; F:GTP diphosphokinase activity; IEA:UniProtKB-EC.
DR GO; GO:0016301; F:kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0015970; P:guanosine tetraphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR CDD; cd05399; NT_Rel-Spo_like; 1.
DR Gene3D; 3.30.460.10; -; 1.
DR InterPro; IPR043519; NT_sf.
DR InterPro; IPR007685; RelA_SpoT.
DR Pfam; PF04607; RelA_SpoT; 1.
DR SMART; SM00954; RelA_SpoT; 1.
DR SUPFAM; SSF81301; SSF81301; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; ATP-binding; GTP-binding; Kinase;
KW Magnesium; Metal-binding; Nucleotide-binding; Reference proteome;
KW Transferase.
FT CHAIN 1..211
FT /note="GTP pyrophosphokinase YjbM"
FT /id="PRO_0000390876"
FT ACT_SITE 139
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:26460002"
FT BINDING 21..28
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="2"
FT /ligand_note="allosteric activator; ligand shared between
FT two neighboring subunits"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 41..42
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="2"
FT /ligand_note="allosteric activator; ligand shared between
FT two neighboring subunits"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 46..48
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26460002,
FT ECO:0007744|PDB:5F2V"
FT BINDING 46..48
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="1"
FT /ligand_note="product"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 52
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26460002,
FT ECO:0007744|PDB:5F2V"
FT BINDING 56..59
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26460002,
FT ECO:0007744|PDB:5F2V"
FT BINDING 59
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="1"
FT /ligand_note="product"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 72
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26460002,
FT ECO:0007744|PDB:5F2V"
FT BINDING 72
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:26460002"
FT BINDING 77
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:26460002,
FT ECO:0007744|PDB:5F2V"
FT BINDING 105
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="1"
FT /ligand_note="product"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 112..114
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="1"
FT /ligand_note="product"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 120
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="1"
FT /ligand_note="product"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 148
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="2"
FT /ligand_note="allosteric activator; ligand shared between
FT two neighboring subunits"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT BINDING 151..155
FT /ligand="guanosine 3'-diphosphate 5'-triphosphate"
FT /ligand_id="ChEBI:CHEBI:142410"
FT /ligand_label="1"
FT /ligand_note="product"
FT /evidence="ECO:0000269|PubMed:26460002,
FT ECO:0007744|PDB:5DED"
FT MUTAGEN 25
FT /note="K->A: No stimulation by (p)ppGpp, protein still
FT forms tetramers."
FT /evidence="ECO:0000269|PubMed:26460002"
FT MUTAGEN 42
FT /note="F->A: No stimulation by (p)ppGpp, protein still
FT forms tetramers."
FT /evidence="ECO:0000269|PubMed:26460002"
FT MUTAGEN 46
FT /note="R->G: Loss of (p)ppGpp synthesis, protein still
FT forms tetramers."
FT /evidence="ECO:0000269|PubMed:26460002"
FT MUTAGEN 139
FT /note="E->V: Loss of (p)ppGpp synthesis, protein still
FT forms tetramers."
FT /evidence="ECO:0000269|PubMed:26460002"
FT MUTAGEN 148
FT /note="N->G: No stimulation by (p)ppGpp, protein still
FT forms tetramers."
FT /evidence="ECO:0000269|PubMed:26460002"
FT HELIX 4..31
FT /evidence="ECO:0007829|PDB:5DEC"
FT STRAND 42..47
FT /evidence="ECO:0007829|PDB:5DEC"
FT HELIX 50..59
FT /evidence="ECO:0007829|PDB:5DEC"
FT HELIX 64..69
FT /evidence="ECO:0007829|PDB:5DEC"
FT STRAND 73..82
FT /evidence="ECO:0007829|PDB:5DEC"
FT HELIX 83..95
FT /evidence="ECO:0007829|PDB:5DEC"
FT STRAND 97..107
FT /evidence="ECO:0007829|PDB:5DEC"
FT HELIX 108..113
FT /evidence="ECO:0007829|PDB:5F2V"
FT STRAND 119..129
FT /evidence="ECO:0007829|PDB:5DEC"
FT STRAND 132..144
FT /evidence="ECO:0007829|PDB:5DEC"
FT HELIX 145..160
FT /evidence="ECO:0007829|PDB:5DEC"
FT TURN 161..163
FT /evidence="ECO:0007829|PDB:5DEC"
FT HELIX 167..195
FT /evidence="ECO:0007829|PDB:5DEC"
SQ SEQUENCE 211 AA; 24704 MW; 8FB2A73CE865FAA2 CRC64;
MDDKQWERFL VPYRQAVEEL KVKLKGIRTL YEYEDDHSPI EFVTGRVKPV ASILEKARRK
SIPLHEIETM QDIAGLRIMC QFVDDIQIVK EMLFARKDFT VVDQRDYIAE HKESGYRSYH
LVVLYPLQTV SGEKHVLVEI QIRTLAMNFW ATIEHSLNYK YSGNIPEKVK LRLQRASEAA
SRLDEEMSEI RGEVQEAQAA FSRKKKGSEQ Q
