Bifunctional (p)ppGpp synthase/hydrolase SpoT - Escherichia coli (strain K12)

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P0AG24 (SPOT_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 72. History...

Clusters with 100%, 90%, 50% identity |

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	spoT
Ordered Locus Names:	b3650, JW3625

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	702 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.7 Ref.10
Catalytic activity	ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate. Guanosine 3',5'-bis(diphosphate) + H₂O = guanosine 5'-diphosphate + diphosphate.
Cofactor	Manganese.
Pathway	Purine metabolism; ppGpp biosynthesis; ppGpp from GDP: step 1/1. Purine metabolism; ppGpp biosynthesis; ppGpp from GTP: step 1/2.
Subunit structure	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. Ref.8 Ref.9
Subcellular location	Cytoplasm. Note: Is associated with pre-50S ribosomal subunits in a salt-dependent manner. Ref.9
Disruption phenotype	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. Ref.7 Ref.10
Sequence similarities	Belongs to the RelA/SpoT family. Contains 1 HD domain.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Manganese
Molecular function	Hydrolase Kinase Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	guanosine tetraphosphate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway nucleobase-containing small molecule interconversion Inferred from mutant phenotype PubMed 319345. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	GTP diphosphokinase activity Inferred from electronic annotation. Source: EC guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity Inferred from direct assay PubMed 365225. Source: EcoCyc kinase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: InterPro phosphoric diester hydrolase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
acpP	P0A6A8	5	EBI-543228,EBI-542566

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 702

702

Bifunctional (p)ppGpp synthase/hydrolase SpoT

PRO_0000166569

Regions

Domain

45 – 144

100

Experimental info

Mutagenesis

D → N: Obviates hydrolysis of ppGpp, moderately decreases biofilm formation, loss of biofilm induction in response to translation inhibitors. Ref.10

Mutagenesis

259

D → N: Obviates synthesis of ppGpp, strongly increases biofilm formation. Ref.10

Mutagenesis

293

D → A: Unable to restore (p)ppGpp synthesis nor complement a relA/spoT double disruption. Ref.6

Mutagenesis

294

Y → I: Synthesizes (p)ppGpp, complements a relA/spoT double disruption.

Sequences

Sequence

Length

Mass (Da)

Tools

P0AG24 [UniParc].

Last modified December 20, 2005. Version 1.
Checksum: A85F70F57D082EE8
Show »

FASTA

702

79,342

        10         20         30         40         50         60 
MYLFESLNQL IQTYLPEDQI KRLRQAYLVA RDAHEGQTRS SGEPYITHPV AVACILAEMK 

        70         80         90        100        110        120 
LDYETLMAAL LHDVIEDTPA TYQDMEQLFG KSVAELVEGV SKLDKLKFRD KKEAQAENFR 

       130        140        150        160        170        180 
KMIMAMVQDI RVILIKLADR THNMRTLGSL RPDKRRRIAR ETLEIYSPLA HRLGIHHIKT 

       190        200        210        220        230        240 
ELEELGFEAL YPNRYRVIKE VVKAARGNRK EMIQKILSEI EGRLQEAGIP CRVSGREKHL 

       250        260        270        280        290        300 
YSIYCKMVLK EQRFHSIMDI YAFRVIVNDS DTCYRVLGQM HSLYKPRPGR VKDYIAIPKA 

       310        320        330        340        350        360 
NGYQSLHTSM IGPHGVPVEV QIRTEDMDQM AEMGVAAHWA YKEHGETSTT AQIRAQRWMQ 

       370        380        390        400        410        420 
SLLELQQSAG SSFEFIESVK SDLFPDEIYV FTPEGRIVEL PAGATPVDFA YAVHTDIGHA 

       430        440        450        460        470        480 
CVGARVDRQP YPLSQPLTSG QTVEIITAPG ARPNAAWLNF VVSSKARAKI RQLLKNLKRD 

       490        500        510        520        530        540 
DSVSLGRRLL NHALGGSRKL NEIPQENIQR ELDRMKLATL DDLLAEIGLG NAMSVVVAKN 

       550        560        570        580        590        600 
LQHGDASIPP ATQSHGHLPI KGADGVLITF AKCCRPIPGD PIIAHVSPGK GLVIHHESCR 

       610        620        630        640        650        660 
NIRGYQKEPE KFMAVEWDKE TAQEFITEIK VEMFNHQGAL ANLTAAINTT TSNIQSLNTE 

       670        680        690        700 
EKDGRVYSAF IRLTARDRVH LANIMRKIRV MPDVIKVTRN RN

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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(1989) [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(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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(2006) [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(1991) [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(2002) [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(2003) [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(2004) [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(2007) [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(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN BIOFILM FORMATION, MUTAGENESIS OF ASP-73 AND ASP-259, DISRUPTION PHENOTYPE. Strain: K12 / MG1655 / AB400.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M24503 Genomic DNA. Translation: AAB00160.1. L10328 Genomic DNA. Translation: AAA62003.1. U00096 Genomic DNA. Translation: AAC76674.1. AP009048 Genomic DNA. Translation: BAE77643.1.
PIR	SHECGD. B30374.
RefSeq	NP_418107.1. NC_000913.2. YP_491784.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0AG24.
SMR	P0AG24. Positions 5-339, 387-448.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-29378N.
IntAct	P0AG24. 59 interactions.
MINT	MINT-1219858.
STRING	511145.b3650.
Proteomic databases
PaxDb	P0AG24.
PRIDE	P0AG24.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC76674; AAC76674; b3650. BAE77643; BAE77643; BAE77643.
GeneID	12930367. 948159.
KEGG	ecj:Y75_p3524. eco:b3650.
PATRIC	32122787. VBIEscCol129921_3770.
Organism-specific databases
EchoBASE	EB0959.
EcoGene	EG10966. spoT.
Phylogenomic databases
eggNOG	COG0317.
HOGENOM	HOG000018299.
KO	K01139.
OMA	RAYFYAE.
ProtClustDB	PRK11092.
Enzyme and pathway databases
BioCyc	EcoCyc:SPOT-MONOMER. ECOL316407:JW3625-MONOMER. MetaCyc:SPOT-MONOMER.
UniPathway	UPA00908; UER00884. UPA00908; UER00886.
Gene expression databases
Genevestigator	P0AG24.
Family and domain databases
Gene3D	3.10.20.30. 1 hit.
InterPro	IPR026020. (p)ppGpp_Synthase. 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]
PANTHER	PTHR21262. PTHR21262. 1 hit.
Pfam	PF01966. HD. 1 hit. PF04607. RelA_SpoT. 1 hit. PF02824. TGS. 1 hit. [Graphical view]
SMART	SM00471. HDc. 1 hit. SM00954. RelA_SpoT. 1 hit. [Graphical view]
SUPFAM	SSF81271. TGS-like. 1 hit.
TIGRFAMs	TIGR00691. spoT_relA. 1 hit.
ProtoNet	Search...

Entry information

Entry name

SPOT_ECOLI

Accession

Primary (citable) accession number: P0AG24
Secondary accession number(s): P17580, Q2M7W3

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	December 20, 2005
Last modified:	May 1, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Including the following 2 domains:

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents