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Protein

Bifunctional (p)ppGpp synthase/hydrolase SpoT

Gene

spoT

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

Functioni

In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response which 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. ppGpp activates transcription of CsrA-antagonistic small RNAs CsrB and CsrC, which downregulate CsrA's action on translation during the stringent response (PubMed:21488981).3 Publications

Catalytic activityi

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

Cofactori

Pathwayi: ppGpp biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes ppGpp from GDP.
Proteins known to be involved in this subpathway in this organism are:
  1. Bifunctional (p)ppGpp synthase/hydrolase SpoT (spoT)
This subpathway is part of the pathway ppGpp biosynthesis, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes ppGpp from GDP, the pathway ppGpp biosynthesis and in Purine metabolism.

Pathwayi: ppGpp biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes ppGpp from GTP.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. GTP pyrophosphokinase (relA), Bifunctional (p)ppGpp synthase/hydrolase SpoT (spoT)
  2. Guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase (gppA)
This subpathway is part of the pathway ppGpp biosynthesis, which is itself part of Purine metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes ppGpp from GTP, the pathway ppGpp biosynthesis and in Purine metabolism.

GO - Molecular functioni

GO - Biological processi

  • guanosine tetraphosphate biosynthetic process Source: UniProtKB-UniPathway
  • nucleobase-containing small molecule interconversion Source: EcoCyc

Keywordsi

Molecular functionHydrolase, Kinase, Transferase
LigandManganese

Enzyme and pathway databases

BioCyciEcoCyc:SPOT-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 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

  • cell wall Source: GO_Central
  • cytosol Source: EcoCyc
  • plasma membrane Source: GO_Central

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) (PubMed:19460094). The ppGpp0 mutant makes decreased levels of CsrA and its inhibitory small RNAs (sRNA) CsrB and CsrC (PubMed:21488981). The double relA/spoT deletion obviates persister cell formation in a hipA7 mutant (PubMed:14622409, PubMed:26051177).4 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi73D → N: Obviates hydrolysis of ppGpp, moderately decreases biofilm formation, loss of biofilm induction in response to translation inhibitors. 1 Publication1
Mutagenesisi259D → N: Obviates synthesis of ppGpp, strongly increases biofilm formation. 1 Publication1
Mutagenesisi293D → A: Unable to restore (p)ppGpp synthesis nor complement a relA/spoT double disruption. 1 Publication1
Mutagenesisi294Y → I: Synthesizes (p)ppGpp, complements a relA/spoT double disruption. 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001665691 – 702Bifunctional (p)ppGpp synthase/hydrolase SpoTAdd BLAST702

Proteomic databases

PaxDbiP0AG24
PRIDEiP0AG24

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
acpPP0A6A86EBI-543228,EBI-542566

Protein-protein interaction databases

BioGridi4259361, 494 interactors
DIPiDIP-29378N
IntActiP0AG24, 61 interactors
STRINGi316385.ECDH10B_3832

Structurei

3D structure databases

ProteinModelPortaliP0AG24
SMRiP0AG24
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini45 – 144HDPROSITE-ProRule annotationAdd BLAST100
Domaini628 – 702ACTPROSITE-ProRule annotationAdd BLAST75

Sequence similaritiesi

Belongs to the RelA/SpoT family.Curated

Phylogenomic databases

eggNOGiENOG4105CWR Bacteria
COG0317 LUCA
HOGENOMiHOG000018299
InParanoidiP0AG24
KOiK01139
OMAiHYYSIYQ
PhylomeDBiP0AG24

Family and domain databases

CDDicd00077 HDc, 1 hit
cd05399 NT_Rel-Spo_like, 1 hit
cd01668 TGS_RelA_SpoT, 1 hit
Gene3Di3.10.20.30, 1 hit
InterProiView protein in InterPro
IPR002912 ACT_dom
IPR012675 Beta-grasp_dom_sf
IPR003607 HD/PDEase_dom
IPR004811 RelA/Spo_fam
IPR007685 RelA_SpoT
IPR004095 TGS
IPR012676 TGS-like
IPR033655 TGS_RelA
PfamiView protein in Pfam
PF13291 ACT_4, 1 hit
PF13328 HD_4, 1 hit
PF04607 RelA_SpoT, 1 hit
PF02824 TGS, 1 hit
SMARTiView protein in SMART
SM00471 HDc, 1 hit
SM00954 RelA_SpoT, 1 hit
SUPFAMiSSF81271 SSF81271, 1 hit
TIGRFAMsiTIGR00691 spoT_relA, 1 hit
PROSITEiView protein in PROSITE
PS51671 ACT, 1 hit
PS51831 HD, 1 hit

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
WP_000280488.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC76674; AAC76674; b3650
BAE77643; BAE77643; BAE77643
GeneIDi948159
KEGGiecj:JW3625
eco:b3650
PATRICifig|1411691.4.peg.3056

Similar proteinsi

Entry informationi

Entry nameiSPOT_ECOLI
AccessioniPrimary (citable) accession number: P0AG24
Secondary accession number(s): P17580, Q2M7W3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: May 23, 2018
This is version 112 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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