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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	ppk
Gene Synonym(s)	ECK2497, b2501, JW2486^[1], JW2486
Product Desc.	Ppk^[2]^[3]; Component of polyphosphate kinase^[2]^[3]; degradosome^[3] Polyphosphate kinase, reversible^[4]
Product Synonyms(s)	polyphosphate kinase, component of RNA degradosome^[1], B2501^[2]^[1], Ppk^[2]^[1] , ECK2497, JW2486, b2501
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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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	ppk
Mnemonic	Polyphosphate kinase
Synonyms	ECK2497, b2501, JW2486^[1], JW2486
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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	56.49 minutes, 56.49 minutes	MG1655: 2621066..2623132 <gbrowseImage> name=NC_000913:2621066..2623132 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2543863..2545929 <gbrowseImage> name=NC_012967:2543863..2545929 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2506871..2508937 <gbrowseImage> name=NC_012759:2506871..2508937 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2621700..2623766 <gbrowseImage> name=NC_007779:2621700..2623766 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2712831..2714897 <gbrowseImage> name=NC_010473:2712831..2714897 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	2621069	Edman degradation	PMID:1331061
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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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
Δppk (Keio:JW2486)	deletion	deletion			PMID:16738554	Shigen CGSC9985^[5]
ppk::Tn5KAN-2 (FB20830)	Insertion at nt 1370 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20830	contains pKD46
Δppk::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
Δppk::kan	deletion		Biolog:respiration	unable to respire Bromosuccinate	PMID:16095938
Δppk::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
Δppk-749::kan					PMID:16738554	CGSC:102436
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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
JW2486	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGGTCAGGAAAAGCTATACAT Primer 2:CCTTCAGGTTGTTCGAGTGATTT
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: 35% ^[6]
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 16% ^[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:EG11510	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11510	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001466	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946971	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1472	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008235	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	Ppk
Synonyms	polyphosphate kinase, component of RNA degradosome^[1], B2501^[2]^[1], Ppk^[2]^[1] , ECK2497, JW2486, b2501
Product description	Ppk^[2]^[3]; Component of polyphosphate kinase^[2]^[3]; degradosome^[3] Polyphosphate kinase, reversible^[4]
EC number (for enzymes)	2.7.4.1^[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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001736	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	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-0997	C	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:0006799	polyphosphate biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00347	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006799	polyphosphate biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003414	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001736	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008976	polyphosphate kinase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00347	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008976	polyphosphate kinase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003414	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008976	polyphosphate kinase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.4.1	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009358	polyphosphate kinase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003414	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:0016301	kinase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0418	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	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 polyphosphate kinase	could be indirect
Protein	aceF		PMID:15690043	Experiment(s):EBI-889424
Protein	lpdA		PMID:15690043	Experiment(s):EBI-889424
Protein	cybC		PMID:16606699	Experiment(s):EBI-1143050
Protein	groL		PMID:16606699	Experiment(s):EBI-1143050
Protein	yghW		PMID:16606699	Experiment(s):EBI-1143050
Protein	sdhA		PMID:16606699	Experiment(s):EBI-1143050
Protein	yibL		PMID:16606699	Experiment(s):EBI-1143050
Protein	Subunits of degradosome	could be indirect
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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
membrane			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 MGQEKLYIEK ELSWLSFNER VLQEAADKSN PLIERMRFLG IYSNNLDEFY KVRFAELKRR IIISEEQGSN SHSRHLLGKI QSRVLKADQE FDGLYNELLL EMARNQIFLI NERQLSVNQQ NWLRHYFKQY LRQHITPILI NPDTDLVQFL KDDYTYLAVE IIRGDTIRYA LLEIPSDKVP RFVNLPPEAP RRRKPMILLD NILRYCLDDI FKGFFDYDAL NAYSMKMTRD AEYDLVHEME ASLMELMSSS LKQRLTAEPV RFVYQRDMPN ALVEVLREKL TISRYDSIVP GGRYHNFKDF INFPNVGKAN LVNKPLPRLR HIWFDKAQFR NGFDAIRERD VLLYYPYHTF EHVLELLRQA SFDPSVLAIK INIYRVAKDS RIIDSMIHAA HNGKKVTVVV ELQARFDEEA NIHWAKRLTE AGVHVIFSAP GLKIHAKLFL ISRKENGEVV RYAHIGTGNF NEKTARLYTD YSLLTADARI TNEVRRVFNF IENPYRPVTF DYLMVSPQNS RRLLYEMVDR EIANAQQGLP SGITLKLNNL VDKGLVDRLY AASSSGVPVN LLVRGMCSLI PNLEGISDNI RAISIVDRYL EHDRVYIFEN GGDKKVYLSS ADWMTRNIDY RIEVATPLLD PRLKQRVLDI IDILFSDTVK ARYIDKELSN RYVPRGNRRK VRAQLAIYDY IKSLEQPE
Length	688
Mol. Wt	80.435 kDa
pI	9.3 (calculated)
Extinction coefficient	79,650 - 79,900 (calc based on 35 Y, 5 W, and 2 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:P0A7B1
Domain	6..682	PF02503 Polyphosphate kinase		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=ppk 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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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
NCBI (Protein) (EcoliWiki Page)	GI:16130426	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946971	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008235	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7B1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11510	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11510	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946971	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001466	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1472	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	Notes	Reference(s)
Protein	Ecoli K-12	27.721+/-0.225	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.047192643	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	257	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	244	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	224	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_000913:2621046..2621086 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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:b2501 (EcoliWiki Page)	NCBI GEO profiles for ppk
microarray	GenExpDB:b2501 (EcoliWiki Page)	Summary of data for ppk 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 ppk Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11510	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1472	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2501
EcoGene	EcoGene:EG11510	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001466	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008235	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
Dictyostelium discoideum	DDB0216190 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PPK	From SHIGELLACYC
E. coli O157	PPK	From ECOO157CYC
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Do-It-Yourself Web Tools

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:56024
Superfamily (EcoliWiki Page)	SUPERFAMILY:56024
Superfamily (EcoliWiki Page)	SUPERFAMILY:140356
Superfamily (EcoliWiki Page)	SUPERFAMILY:143724
Pfam (EcoliWiki Page)	PF02503 Polyphosphate kinase
EcoCyc	EcoCyc:EG11510	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11510	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001466	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1472	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008235	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 ^3.5 ^3.6 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).

ppk:On One Page

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Notes

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 ppk Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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