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Protein

Bifunctional (p)ppGpp synthase/hydrolase SpoT

Gene

spoT

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes both the synthesis and degradation of ppGpp. The second messengers ppGpp and c-di-GMP together control biofilm formation in response to translational stress; ppGpp represses biofilm formation while c-di-GMP induces it.2 Publications

Catalytic activityi

ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
Guanosine 3',5'-bis(diphosphate) + H2O = guanosine 5'-diphosphate + diphosphate.

Cofactori

Pathwayi

GO - Molecular functioni

  1. amino acid binding Source: InterPro
  2. GTP diphosphokinase activity Source: UniProtKB-EC
  3. guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity Source: EcoCyc
  4. kinase activity Source: UniProtKB-KW

GO - Biological processi

  1. guanosine tetraphosphate biosynthetic process Source: UniProtKB-UniPathway
  2. nucleobase-containing small molecule interconversion Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Kinase, Transferase

Keywords - Ligandi

Manganese

Enzyme and pathway databases

BioCyciEcoCyc:SPOT-MONOMER.
ECOL316407:JW3625-MONOMER.
MetaCyc:SPOT-MONOMER.
UniPathwayiUPA00908; UER00884.
UPA00908; UER00886.

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional (p)ppGpp synthase/hydrolase SpoT
Including the following 2 domains:
GTP pyrophosphokinase (EC:2.7.6.5)
Alternative name(s):
(p)ppGpp synthase
ATP:GTP 3'-pyrophosphotransferase
Stringent response-like protein
ppGpp synthase II
Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (EC:3.1.7.2)
Alternative name(s):
Penta-phosphate guanosine-3'-pyrophosphohydrolase
Short name:
(ppGpp)ase
Gene namesi
Name:spoT
Ordered Locus Names:b3650, JW3625
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10966. spoT.

Subcellular locationi

Cytoplasm 1 Publication
Note: Is associated with pre-50S ribosomal subunits in a salt-dependent manner.

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

In the presence of wild-type relA, spoT cannot be deleted because ppGpp accumulation is toxic. In the double relA/spoT deletion (a ppGpp0 mutant) there is a very large increase in biofilm formation (in a csrA-disrupted background). The double relA/spoT deletion obviates persister cell formation in a hipA7 mutant.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi73 – 731D → N: Obviates hydrolysis of ppGpp, moderately decreases biofilm formation, loss of biofilm induction in response to translation inhibitors. 1 Publication
Mutagenesisi259 – 2591D → N: Obviates synthesis of ppGpp, strongly increases biofilm formation. 1 Publication
Mutagenesisi293 – 2931D → A: Unable to restore (p)ppGpp synthesis nor complement a relA/spoT double disruption. 1 Publication
Mutagenesisi294 – 2941Y → I: Synthesizes (p)ppGpp, complements a relA/spoT double disruption.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 702702Bifunctional (p)ppGpp synthase/hydrolase SpoTPRO_0000166569Add
BLAST

Proteomic databases

PaxDbiP0AG24.
PRIDEiP0AG24.

Expressioni

Gene expression databases

GenevestigatoriP0AG24.

Interactioni

Subunit structurei

Interacts with ObgE/CgtA (AC P42641); this association is not required for pre-50S ribosome binding. Under both amino acid and carbon starvation conditions about half of the protein dissociates from the ribosome.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
acpPP0A6A85EBI-543228,EBI-542566

Protein-protein interaction databases

DIPiDIP-29378N.
IntActiP0AG24. 59 interactions.
MINTiMINT-1219858.
STRINGi511145.b3650.

Structurei

3D structure databases

SMRiP0AG24. Positions 5-339, 387-448.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini45 – 144100HDAdd
BLAST
Domaini628 – 70275ACTPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the RelA/SpoT family.Curated
Contains 1 ACT domain.PROSITE-ProRule annotation
Contains 1 HD domain.Curated

Phylogenomic databases

eggNOGiCOG0317.
HOGENOMiHOG000018299.
InParanoidiP0AG24.
KOiK01139.
OMAiLDWLNFV.
OrthoDBiEOG6SV551.
PhylomeDBiP0AG24.

Family and domain databases

Gene3Di3.10.20.30. 1 hit.
InterProiIPR002912. ACT_dom.
IPR012675. Beta-grasp_dom.
IPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR004811. RelA/Spo_fam.
IPR007685. RelA_SpoT.
IPR004095. TGS.
IPR012676. TGS-like.
[Graphical view]
PfamiPF01966. HD. 1 hit.
PF04607. RelA_SpoT. 1 hit.
PF02824. TGS. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
SM00954. RelA_SpoT. 1 hit.
[Graphical view]
SUPFAMiSSF81271. SSF81271. 1 hit.
TIGRFAMsiTIGR00691. spoT_relA. 1 hit.
PROSITEiPS51671. ACT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AG24-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYLFESLNQL IQTYLPEDQI KRLRQAYLVA RDAHEGQTRS SGEPYITHPV
60 70 80 90 100
AVACILAEMK LDYETLMAAL LHDVIEDTPA TYQDMEQLFG KSVAELVEGV
110 120 130 140 150
SKLDKLKFRD KKEAQAENFR KMIMAMVQDI RVILIKLADR THNMRTLGSL
160 170 180 190 200
RPDKRRRIAR ETLEIYSPLA HRLGIHHIKT ELEELGFEAL YPNRYRVIKE
210 220 230 240 250
VVKAARGNRK EMIQKILSEI EGRLQEAGIP CRVSGREKHL YSIYCKMVLK
260 270 280 290 300
EQRFHSIMDI YAFRVIVNDS DTCYRVLGQM HSLYKPRPGR VKDYIAIPKA
310 320 330 340 350
NGYQSLHTSM IGPHGVPVEV QIRTEDMDQM AEMGVAAHWA YKEHGETSTT
360 370 380 390 400
AQIRAQRWMQ SLLELQQSAG SSFEFIESVK SDLFPDEIYV FTPEGRIVEL
410 420 430 440 450
PAGATPVDFA YAVHTDIGHA CVGARVDRQP YPLSQPLTSG QTVEIITAPG
460 470 480 490 500
ARPNAAWLNF VVSSKARAKI RQLLKNLKRD DSVSLGRRLL NHALGGSRKL
510 520 530 540 550
NEIPQENIQR ELDRMKLATL DDLLAEIGLG NAMSVVVAKN LQHGDASIPP
560 570 580 590 600
ATQSHGHLPI KGADGVLITF AKCCRPIPGD PIIAHVSPGK GLVIHHESCR
610 620 630 640 650
NIRGYQKEPE KFMAVEWDKE TAQEFITEIK VEMFNHQGAL ANLTAAINTT
660 670 680 690 700
TSNIQSLNTE EKDGRVYSAF IRLTARDRVH LANIMRKIRV MPDVIKVTRN

RN
Length:702
Mass (Da):79,342
Last modified:December 20, 2005 - v1
Checksum:iA85F70F57D082EE8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24503 Genomic DNA. Translation: AAB00160.1.
L10328 Genomic DNA. Translation: AAA62003.1.
U00096 Genomic DNA. Translation: AAC76674.1.
AP009048 Genomic DNA. Translation: BAE77643.1.
PIRiB30374. SHECGD.
RefSeqiNP_418107.1. NC_000913.3.
YP_491784.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC76674; AAC76674; b3650.
BAE77643; BAE77643; BAE77643.
GeneIDi12930367.
948159.
KEGGiecj:Y75_p3524.
eco:b3650.
PATRICi32122787. VBIEscCol129921_3770.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24503 Genomic DNA. Translation: AAB00160.1.
L10328 Genomic DNA. Translation: AAA62003.1.
U00096 Genomic DNA. Translation: AAC76674.1.
AP009048 Genomic DNA. Translation: BAE77643.1.
PIRiB30374. SHECGD.
RefSeqiNP_418107.1. NC_000913.3.
YP_491784.1. NC_007779.1.

3D structure databases

SMRiP0AG24. Positions 5-339, 387-448.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-29378N.
IntActiP0AG24. 59 interactions.
MINTiMINT-1219858.
STRINGi511145.b3650.

Proteomic databases

PaxDbiP0AG24.
PRIDEiP0AG24.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76674; AAC76674; b3650.
BAE77643; BAE77643; BAE77643.
GeneIDi12930367.
948159.
KEGGiecj:Y75_p3524.
eco:b3650.
PATRICi32122787. VBIEscCol129921_3770.

Organism-specific databases

EchoBASEiEB0959.
EcoGeneiEG10966. spoT.

Phylogenomic databases

eggNOGiCOG0317.
HOGENOMiHOG000018299.
InParanoidiP0AG24.
KOiK01139.
OMAiLDWLNFV.
OrthoDBiEOG6SV551.
PhylomeDBiP0AG24.

Enzyme and pathway databases

UniPathwayiUPA00908; UER00884.
UPA00908; UER00886.
BioCyciEcoCyc:SPOT-MONOMER.
ECOL316407:JW3625-MONOMER.
MetaCyc:SPOT-MONOMER.

Miscellaneous databases

PROiP0AG24.

Gene expression databases

GenevestigatoriP0AG24.

Family and domain databases

Gene3Di3.10.20.30. 1 hit.
InterProiIPR002912. ACT_dom.
IPR012675. Beta-grasp_dom.
IPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR004811. RelA/Spo_fam.
IPR007685. RelA_SpoT.
IPR004095. TGS.
IPR012676. TGS-like.
[Graphical view]
PfamiPF01966. HD. 1 hit.
PF04607. RelA_SpoT. 1 hit.
PF02824. TGS. 1 hit.
[Graphical view]
SMARTiSM00471. HDc. 1 hit.
SM00954. RelA_SpoT. 1 hit.
[Graphical view]
SUPFAMiSSF81271. SSF81271. 1 hit.
TIGRFAMsiTIGR00691. spoT_relA. 1 hit.
PROSITEiPS51671. ACT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the spoT gene of Escherichia coli."
    Sarubbi E., Rudd K.E., Xiao H., Ikehara K., Kalman M., Cashel M.
    J. Biol. Chem. 264:15074-15082(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
    Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
    Genomics 16:551-561(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations."
    Xiao H., Kalman M., Ikehara K., Zemel S., Glaser G., Cashel M.
    J. Biol. Chem. 266:5980-5990(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROBABLE (P)PPGPP SYNTHESIS ACTIVITY.
  6. "Identification of an indispensable amino acid for ppGpp synthesis of Escherichia coli SpoT protein."
    Fujita C., Maeda M., Fujii T., Iwamoto R., Ikehara K.
    Biosci. Biotechnol. Biochem. 66:2735-2738(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: PPGPP SYNTHASE ACTIVITY, MUTAGENESIS OF ASP-293.
    Strain: CF8295.
  7. "Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis."
    Korch S.B., Henderson T.A., Hill T.M.
    Mol. Microbiol. 50:1199-1213(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PERSISTENCE, DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / ATCC 47076.
  8. "The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase."
    Wout P., Pu K., Sullivan S.M., Reese V., Zhou S., Lin B., Maddock J.R.
    J. Bacteriol. 186:5249-5257(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH OBGE/CGTA.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  9. "G-protein control of the ribosome-associated stress response protein SpoT."
    Jiang M., Sullivan S.M., Wout P.K., Maddock J.R.
    J. Bacteriol. 189:6140-6147(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, LARGE RIBOSOMAL SUBUNIT ASSOCIATION, CHARACTERIZATION UNDER AMINO ACID OR CARBON STARVATION.
    Strain: K12.
  10. "Second messenger signalling governs Escherichia coli biofilm induction upon ribosomal stress."
    Boehm A., Steiner S., Zaehringer F., Casanova A., Hamburger F., Ritz D., Keck W., Ackermann M., Schirmer T., Jenal U.
    Mol. Microbiol. 72:1500-1516(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN BIOFILM FORMATION, MUTAGENESIS OF ASP-73 AND ASP-259, DISRUPTION PHENOTYPE.
    Strain: K12 / MG1655 / AB400.

Entry informationi

Entry nameiSPOT_ECOLI
AccessioniPrimary (citable) accession number: P0AG24
Secondary accession number(s): P17580, Q2M7W3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: April 1, 2015
This is version 88 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.