ppa:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

ppa

Gene Synonym(s)

ECK4222, b4226, JW4185[1], JW4185

Product Desc.

Ppa[2][3];

Component of inorganic pyrophosphatase[3]

Inorganic pyrophosphatase; binds Zn(II); homohexameric, dimer of trimers[4]

Product Synonyms(s)

inorganic pyrophosphatase[1], B4226[2][1], Ppa[2][1] , ECK4222, JW4185, b4226

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ppA[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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

ppa

Mnemonic

Pyrophosphatase

Synonyms

ECK4222, b4226, JW4185[1], JW4185

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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

95.85 minutes 

MG1655: 4447675..4447145
<gbrowseImage> name=NC_000913:4447145..4447675 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4432902..4432372
<gbrowseImage> name=NC_012967:4432372..4432902 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4385880..4386410
<gbrowseImage> name=NC_012759:4385880..4386410 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4454332..4453802
<gbrowseImage> name=NC_007779:4453802..4454332 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4548037..4547507
<gbrowseImage> name=NC_010473:4547507..4548037 source=DH10B preset=GeneLocation </gbrowseImage>

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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

4447148

Edman degradation

PMID:9298646
PMID:9740056


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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

ppaD103V

D103V

No activity

seeded from UniProt:P0A7A9

ppaK105I

K105I

No activity

seeded from UniProt:P0A7A9

ppaK105R

K105R

3% activity

seeded from UniProt:P0A7A9

ppaY142F

Y142F

22% activity

seeded from UniProt:P0A7A9

ppaE21D

E21D

16% activity

seeded from UniProt:P0A7A9

ppaK30R

K30R

2% activity

seeded from UniProt:P0A7A9

ppaE32D

E32D

6% activity

seeded from UniProt:P0A7A9

ppaR44K

R44K

10% activity

seeded from UniProt:P0A7A9

ppaY52F

Y52F

64% activity

seeded from UniProt:P0A7A9

ppaY56F

Y56F

7% activity

seeded from UniProt:P0A7A9

ppaD66E

D66E

6% activity

seeded from UniProt:P0A7A9

ppaD68E

D68E

1% activity

seeded from UniProt:P0A7A9

ppaD71E

D71E

No activity

seeded from UniProt:P0A7A9

ppaD98E

D98E

22% activity

seeded from UniProt:P0A7A9

ppaD98V

D98V

No activity

seeded from UniProt:P0A7A9

ppaE99V

E99V

33% activity

seeded from UniProt:P0A7A9

ppaD103E

D103E

3% activity

seeded from UniProt:P0A7A9

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Notes

Genetic Interactions

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<protect>

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

JW4185

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCTTACTCAACGTCCCTGC

Primer 2:CCTTTATTCTTTGCGCGCTCGAA

E1H3

Kohara Phage

Genobase

PMID:3038334

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[5]

est. P1 cotransduction: 93% [6]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[5]

est. P1 cotransduction: % [6]
Synonyms:zjj-202::Tn10, zji-202::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:EG10755

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10755

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000746

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948748

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0748

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013824

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Ppa

Synonyms

inorganic pyrophosphatase[1], B4226[2][1], Ppa[2][1] , ECK4222, JW4185, b4226

Product description

Ppa[2][3];

Component of inorganic pyrophosphatase[3]

Inorganic pyrophosphatase; binds Zn(II); homohexameric, dimer of trimers[4]

EC number (for enzymes)
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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:0000287

magnesium ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00209

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008162

F

Seeded from EcoCyc (v14.0)

complete

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:0004427

inorganic diphosphatase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00209

F

Seeded from EcoCyc (v14.0)

complete

GO:0004427

inorganic diphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008162

F

Seeded from EcoCyc (v14.0)

complete

GO:0004427

inorganic diphosphatase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.6.1.1

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:0006796

phosphate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008162

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

PMID:11985624

IDA: Inferred from Direct Assay

F

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 inorganic pyrophosphatase

could be indirect

Protein

dnaK

PMID:15690043

Experiment(s):EBI-889390

Protein

dnaN

PMID:15690043

Experiment(s):EBI-889390

Protein

groL

PMID:15690043

Experiment(s):EBI-889390

Protein

hldD

PMID:15690043

Experiment(s):EBI-889390

Protein

rplD

PMID:15690043

Experiment(s):EBI-889390, EBI-894403

Protein

tufA

PMID:15690043

Experiment(s):EBI-889390

Protein

tig

PMID:15690043

Experiment(s):EBI-889390, EBI-894403

Protein

atoD

PMID:15690043

Experiment(s):EBI-894403

Protein

katG

PMID:15690043

Experiment(s):EBI-894403

Protein

rplC

PMID:15690043

Experiment(s):EBI-894403

Protein

rplI

PMID:15690043

Experiment(s):EBI-894403

Protein

rplM

PMID:15690043

Experiment(s):EBI-894403

Protein

rplN

PMID:15690043

Experiment(s):EBI-894403

Protein

rplS

PMID:15690043

Experiment(s):EBI-894403

Protein

rplV

PMID:15690043

Experiment(s):EBI-894403

Protein

rpmB

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsB

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsC

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsE

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsG

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsH

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsN

PMID:15690043

Experiment(s):EBI-894403

Protein

rpsT

PMID:15690043

Experiment(s):EBI-894403

Protein

secB

PMID:15690043

Experiment(s):EBI-894403

Protein

slyD

PMID:15690043

Experiment(s):EBI-894403

Protein

ybgQ

PMID:15690043

Experiment(s):EBI-894403

Protein

acpT

PMID:15690043

Experiment(s):EBI-894403

Protein

actP

PMID:15690043

Experiment(s):EBI-894403

Protein

yjgD

PMID:15690043

Experiment(s):EBI-894403

Protein

degQ

PMID:16606699

Experiment(s):EBI-1147698

Protein

msrA

PMID:16606699

Experiment(s):EBI-1147698

Protein

rplJ

PMID:16606699

Experiment(s):EBI-1147698

Protein

rhlE

PMID:16606699

Experiment(s):EBI-1147698

Protein

dadA

PMID:16606699

Experiment(s):EBI-1147698

Protein

hemG

PMID:16606699

Experiment(s):EBI-1147698

Protein

rraB

PMID:19402753

LCMS(ID Probability):99.0

Protein

groL

PMID:19402753

MALDI(Z-score):17.053160

Protein

secB

PMID:19402753

LCMS(ID Probability):99.0

Protein

katG

PMID:19402753

LCMS(ID Probability):99.0

Protein

tig

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

kdsB

PMID:19402753

MALDI(Z-score):39.758856

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

Protein

waaA

PMID:19402753

MALDI(Z-score):37.837893

Protein

coaD

PMID:19402753

MALDI(Z-score):25.440462

Protein

ybgQ

PMID:19402753

LCMS(ID Probability):99.0

Protein

actP

PMID:19402753

LCMS(ID Probability):99.0

Protein

acpT

PMID:19402753

LCMS(ID Probability):99.0

Protein

atoD

PMID:19402753

LCMS(ID Probability):99.0

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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 

MSLLNVPAGK DLPEDIYVVI EIPANADPIK YEIDKESGAL FVDRFMSTAM FYPCNYGYIN
HTLSLDGDPV DVLVPTPYPL QPGSVIRCRP VGVLKMTDEA GEDAKLVAVP HSKLSKEYDH
IKDVNDLPEL LKAQIAHFFE HYKDLEKGKW VKVEGWENAE AAKAEIVASF ERAKNK
Length

176

Mol. Wt

19.703 kDa

pI

5.0 (calculated)

Extinction coefficient

22,920 - 23,170 (calc based on 8 Y, 2 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:P0A7A9

Modification Site

142

phosphorylation site at Y142

probability greater than 75%

PMID:17938405

Domain

17..175

PF00719 Inorganic pyrophosphatase

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=ppa 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:16132048

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948748

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013824

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7A9

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10755

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10755

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948748

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000746

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0748

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

E. coli K-12 MC4100

7.16E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

397.635+/-2.229

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.19839+/-0.01035

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.716981132

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 EMG2

5480

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M31�2

PMID: 9298646

Protein

E. coli K-12 EMG2

500

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: M97-l

PMID: 9298646

Protein

E. coli K-12 MG1655

66605

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

16471

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

33274

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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<protect>

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

Transcription unit(s)

ppA

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Figure courtesy of RegulonDB

</protect>

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_000913:4447655..4447695 source=MG1655 flip=1 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

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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:b4226 (EcoliWiki Page)

NCBI GEO profiles for ppa

microarray

GenExpDB:b4226 (EcoliWiki Page)

Summary of data for ppa 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

GFP Fusion

Intergenic region (4447154..4447568) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ15; Well:E12[7]

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Notes

Accessions Related to ppa Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10755

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0748

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4226

EcoGene

EcoGene:EG10755

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000746

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013824

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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

Anopheles gambiae

  • ENSANGP00000000911 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G01050 (score: 1.000; bootstrap: 100%)
  • AT2G18230 (score: 1.000; bootstrap: 100%)
  • AT4G01480 (score: 1.000; bootstrap: 100%)
  • AT2G46860 (score: 0.874)
  • AT3G53620 (score: 0.760)

From Inparanoid:20070104

Oryza gramene

  • O48556 (score: 1.000; bootstrap: 100%)
  • Q7XTL6 (score: 0.938)
  • Q56US1 (score: 0.894)
  • Q75HX3 (score: 0.860)
  • O23979 (score: 0.820)
  • Q5N9F4 (score: 0.792)
  • Q75L10 (score: 0.745)
  • Q6YVH9 (score: 0.717)
  • Q9ZSU9 (score: 0.693)
  • Q5JL11 (score: 0.661)
  • Q948I7 (score: 0.584)
  • Q7XEV0 (score: 0.584)
  • O22537 (score: 0.522)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000004026 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

PPA

From SHIGELLACYC

E. coli O157

PPA

From ECOO157CYC

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Do-It-Yourself Web Tools

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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:50324

Panther (EcoliWiki Page)

PTHR10286:SF0

Pfam (EcoliWiki Page)

PF00719 Inorganic pyrophosphatase

EcoCyc

EcoCyc:EG10755

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10755

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000746

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0748

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013824

Escherichia coli str. K-12 substr. MG1655

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  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

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