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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	ppx
Gene Synonym(s)	ECK2498, b2502, JW2487^[1], JW2487
Product Desc.	Ppx^[2]^[3]; Component of exopolyphosphatase^[2]^[3] Exopolyphosphatase; inhibited by pppGpp and ppGpp, also has guanosine pentaphosphatase activity^[4]
Product Synonyms(s)	exopolyphosphatase^[1], B2502^[2]^[1], Ppx^[2]^[1] , ECK2498, JW2487, b2502
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ppk-ppx^[2]
Regulation/Activity
Quick Links
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Notes

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PDB structure from O157:H7 has identical sequence as K-12. Competitive ihibition of Ppx by pppGpp during amino acid (relA-dependent) and phosphate starvation (spoT-dependent) apparently causes a sharp increase in cellular polyphosphate (Kuroda, 1997).^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	ppx
Mnemonic	Exopolyphosphatase
Synonyms	ECK2498, b2502, JW2487^[1], JW2487
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	56.54 minutes	MG1655: 2623137..2624678 <gbrowseImage> name=NC_000913:2623137..2624678 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2545934..2547475 <gbrowseImage> name=NC_012967:2545934..2547475 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2508942..2510483 <gbrowseImage> name=NC_012759:2508942..2510483 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2623771..2625312 <gbrowseImage> name=NC_007779:2623771..2625312 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2714902..2716443 <gbrowseImage> name=NC_010473:2714902..2716443 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	2623140	Edman degradation	PMID:8380170
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Reference	Availability	Comments
Δppx (Keio:JW2487)	deletion	deletion	PMID:16738554	Shigen CGSC9986^[5]
ppx::Tn5KAN-2 (FB20831)	Insertion at nt 1447 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20831	contains pKD46
ppx::Tn5KAN-2 (FB20832)	Insertion at nt 1447 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20832	does not contain pKD46
Δppx-750::kan			PMID:16738554	CGSC:102442
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW2487	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCAATACACGATAAATCCCC Primer 2:CCAGCGGCGATTTCTGGTGTACT
10H6	Kohara Phage	Genobase	PMID:3038334
5A11	Kohara Phage	Genobase	PMID:3038334
8E3	Kohara Phage	Genobase	PMID:3038334
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 32% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 18% ^[6] Synonyms:zff-208::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11403	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11403	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001369	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946970	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1375	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008238	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	Ppx
Synonyms	exopolyphosphatase^[1], B2502^[2]^[1], Ppx^[2]^[1] , ECK2498, JW2487, b2502
Product description	Ppx^[2]^[3]; Component of exopolyphosphatase^[2]^[3] Exopolyphosphatase; inhibited by pppGpp and ppGpp, also has guanosine pentaphosphatase activity^[4]
EC number (for enzymes)	3.6.1.11^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004309	exopolyphosphatase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.6.1.11	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of exopolyphosphatase	could be indirect
Protein	nadE		PMID:16606699	Experiment(s):EBI-1143057
Protein	napC		PMID:16606699	Experiment(s):EBI-1143057
Protein	galS		PMID:16606699	Experiment(s):EBI-1143057
Protein	yciH		PMID:16606699	Experiment(s):EBI-1143057
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
cytoplasm			From EcoCyc^[3]
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MPIHDKSPRP QEFAAVDLGS NSFHMVIARV VDGAMQIIGR LKQRVHLADG LGPDNMLSEE AMTRGLNCLS LFAERLQGFS PASVCIVGTH TLRQALNATD FLKRAEKVIP YPIEIISGNE EARLIFMGVE HTQPEKGRKL VIDIGGGSTE LVIGENFEPI LVESRRMGCV SFAQLYFPGG VINKENFQRA RMAAAQKLET LTWQFRIQGW NVAMGASGTI KAAHEVLMEM GEKDGIITPE RLEKLVKEVL RHRNFASLSL PGLSEERKTV FVPGLAILCG VFDALAIREL RLSDGALREG VLYEMEGRFR HQDVRSRTAS SLANQYHIDS EQARRVLDTT MQMYEQWREQ QPKLAHPQLE ALLRWAAMLH EVGLNINHSG LHRHSAYILQ NSDLPGFNQE QQLMMATLVR YHRKAIKLDD LPRFTLFKKK QFLPLIQLLR LGVLLNNQRQ ATTTPPTLTL ITDDSHWTLR FPHDWFSQNA LVLLDLEKEQ EYWEGVAGWR LKIEEESTPE IAA
Length	513
Mol. Wt	58.136 kDa
pI	7.1 (calculated)
Extinction coefficient	55,920 - 56,420 (calc based on 8 Y, 8 W, and 4 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Initiator Methionine	1	Removed	UniProt:P0AFL6
Domain	26..309	PF02541 Ppx/GppA phosphatase family		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ppx taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16130427	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946970	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008238	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFL6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11403	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11403	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946970	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001369	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1375	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MG1655	415	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	250	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	218	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
ppk-ppx
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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:2623117..2623157 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b2502 (EcoliWiki Page)	NCBI GEO profiles for ppx
microarray	GenExpDB:b2502 (EcoliWiki Page)	Summary of data for ppx from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to ppx Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11403	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1375	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2502
EcoGene	EcoGene:EG11403	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001369	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008238	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	YP_026252 (score: 0.225) AT1G09190 (score: 1.000; bootstrap: 100%) AT5G56310 (score: 0.092) AT2G20540 (score: 0.089) AT3G04750 (score: 0.082) AT5G15300 (score: 0.082) AT4G14820 (score: 0.080) AT5G08510 (score: 0.080) AT2G22410 (score: 0.078) AT1G33350 (score: 0.076) AT5G48910 (score: 0.076) AT4G37380 (score: 0.074) AT2G29760 (score: 0.073) AT1G06145 (score: 0.072) AT5G59200 (score: 0.072) AT5G44230 (score: 0.072) AT2G13600 (score: 0.072) AT5G66520 (score: 0.070) AT1G05750 (score: 0.069) AT3G05240 (score: 0.069) AT1G13410 (score: 0.068) AT5G40405 (score: 0.068) AT2G42920 (score: 0.066) AT2G44880 (score: 0.066) AT5G59600 (score: 0.066) AT3G62890 (score: 0.065) AT3G15930 (score: 0.063) AT1G25360 (score: 0.063) AT5G15340 (score: 0.063) AT5G06540 (score: 0.063) AT2G21090 (score: 0.063) AT2G22070 (score: 0.062) AT1G74630 (score: 0.062) AT4G18840 (score: 0.062) AT2G36730 (score: 0.062) AT3G29230 (score: 0.061) AT3G49710 (score: 0.059) AT1G17630 (score: 0.059) AT1G20230 (score: 0.058) AT2G33760 (score: 0.058) AT1G28690 (score: 0.058) AT2G02980 (score: 0.057) AT1G77170 (score: 0.056) AT4G14050 (score: 0.055) AT4G35130 (score: 0.055) AT3G11460 (score: 0.055) AT2G01510 (score: 0.055) AT1G06140 (score: 0.055) AT1G59720 (score: 0.054) AT5G61800 (score: 0.054) AT4G01030 (score: 0.053) AT3G46790 (score: 0.053) AT5G37570 (score: 0.053) AT1G50270 (score: 0.052) AT3G12770 (score: 0.052) AT1G04840 (score: 0.052) AT4G16835 (score: 0.050) AT3G13770 (score: 0.050)	From Inparanoid:20070104
Saccharomyces cerevisiae	YP_026252 (score: 1.000; bootstrap: 100%) YGL252C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PPX	From SHIGELLACYC
E. coli O157	PPX	From ECOO157CYC
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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:53067
Superfamily (EcoliWiki Page)	SUPERFAMILY:53067
Superfamily (EcoliWiki Page)	SUPERFAMILY:109604
Pfam (EcoliWiki Page)	PF02541 Ppx/GppA phosphatase family
EcoCyc	EcoCyc:EG11403	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11403	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001369	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1375	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008238	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

ppx:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ppx Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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