ppc: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

ppc

Gene Synonym(s)

ECK3947, b3956, JW3928, asp, glu, pepC[1]

Product Desc.

Ppc[2][3];

Component of phosphoenolpyruvate carboxylase[2][3]

Phosphoenolpyruvate carboxylase; monomeric[4]

Product Synonyms(s)

phosphoenolpyruvate carboxylase[1], B3956[2][1], Glu[2][1], Asp[2][1], Ppc[2][1] , asp, ECK3947, glu, JW3928, b3956

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ppc[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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Mutant has reduced growth rate with little acetate excreation, decrease glucose consumption and a decreased carbon dioxide evolution rate.[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

ppc

Mnemonic

PEP carboxylase

Synonyms

ECK3947, b3956, JW3928, asp, glu, pepC[1]

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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

89.41 minutes, 89.41 minutes 

MG1655: 4151121..4148470
<gbrowseImage> name=NC_000913:4148470..4151121 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4133205..4130554
<gbrowseImage> name=NC_012967:4130554..4133205 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4038139..4040790
<gbrowseImage> name=NC_012759:4038139..4040790 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3483583..3486234
<gbrowseImage> name=NC_007779:3483583..3486234 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4250818..4248167
<gbrowseImage> name=NC_010473:4248167..4250818 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
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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

ppcR587S

R587S

Loss of activity

seeded from UniProt:P00864

ppcH579P

H579P

5.4% of wild-type activity

seeded from UniProt:P00864

ppcH579N

H579N

29% of wild-type activity

seeded from UniProt:P00864

ppcH138N

H138N

Loss of activity

seeded from UniProt:P00864

Δppc (Keio:JW3928)

deletion

deletion

PMID:16738554

Shigen
CGSC10837[5]

Δppc::kan

deletion

Biolog:respiration

unable to respire Dextrin

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire D-Sorbitol

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire DL-a-Glycerol

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire D-Galactoniate

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire D-Galacturonate

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire D-Glucuronate

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire Glucuronamide

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire L-Serine

PMID:16095938

Δppc::kan

deletion

Biolog:respiration

unable to respire Uridine

PMID:16095938

ppc-2

PMID:13791860 PMID:4874804 PMID:14292146

CGSC:7662

ppc-1

PMID:4874804 PMID:14292146

CGSC:7826

ppc-3

CGSC:10656

ppc-5::kan

CGSC:76204

Δppc-742::kan

PMID:16738554

CGSC:102416


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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

JW3928

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAACGAACAATATTCCGCATT

Primer 2:CCGCCGGTATTACGCATACCTGC

4G11

Kohara Phage

Genobase

PMID:3038334

8H10

Kohara Phage

Genobase

PMID:3038334

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[5]

est. P1 cotransduction: 84% [6]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

argE86::Tn10

Linked marker

CAG12185 = CGSC7471[5]

est. P1 cotransduction: 88% [6]

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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:EG10756

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10756

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000747

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948457

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0749

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012950

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

Ppc

Synonyms

phosphoenolpyruvate carboxylase[1], B3956[2][1], Glu[2][1], Asp[2][1], Ppc[2][1] , asp, ECK3947, glu, JW3928, b3956

Product description

Ppc[2][3];

Component of phosphoenolpyruvate carboxylase[2][3]

Phosphoenolpyruvate carboxylase; monomeric[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015813

F

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00595

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001449

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018129

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0816

P

Seeded from EcoCyc (v14.0)

complete

GO:0008964

phosphoenolpyruvate carboxylase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00595

F

Seeded from EcoCyc (v14.0)

complete

GO:0008964

phosphoenolpyruvate carboxylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001449

F

Seeded from EcoCyc (v14.0)

complete

GO:0008964

phosphoenolpyruvate carboxylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018129

F

Seeded from EcoCyc (v14.0)

complete

GO:0008964

phosphoenolpyruvate carboxylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.1.31

F

Seeded from EcoCyc (v14.0)

complete

GO:0015977

carbon fixation

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00595

P

Seeded from EcoCyc (v14.0)

complete

GO:0015977

carbon fixation

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0120

P

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

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 phosphoenolpyruvate carboxylase

could be indirect

Protein

uvrA

PMID:16606699

Experiment(s):EBI-1147140

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

gcvP

PMID:19402753

LCMS(ID Probability):99.6

Protein

glcB

PMID:19402753

LCMS(ID Probability):99.3

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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
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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 

MNEQYSALRS NVSMLGKVLG ETIKDALGEH ILERVETIRK LSKSSRAGND ANRQELLTTL
QNLSNDELLP VARAFSQFLN LANTAEQYHS ISPKGEAASN PEVIARTLRK LKNQPELSED
TIKKAVESLS LELVLTAHPT EITRRTLIHK MVEVNACLKQ LDNKDIADYE HNQLMRRLRQ
LIAQSWHTDE IRKLRPSPVD EAKWGFAVVE NSLWQGVPNY LRELNEQLEE NLGYKLPVEF
VPVRFTSWMG GDRDGNPNVT ADITRHVLLL SRWKATDLFL KDIQVLVSEL SMVEATPELL
ALVGEEGAAE PYRYLMKNLR SRLMATQAWL EARLKGEELP KPEGLLTQNE ELWEPLYACY
QSLQACGMGI IANGDLLDTL RRVKCFGVPL VRIDIRQEST RHTEALGELT RYLGIGDYES
WSEADKQAFL IRELNSKRPL LPRNWQPSAE TREVLDTCQV IAEAPQGSIA AYVISMAKTP
SDVLAVHLLL KEAGIGFAMP VAPLFETLDD LNNANDVMTQ LLNIDWYRGL IQGKQMVMIG
YSDSAKDAGV MAASWAQYQA QDALIKTCEK AGIELTLFHG RGGSIGRGGA PAHAALLSQP
PGSLKGGLRV TEQGEMIRFK YGLPEITVSS LSLYTGAILE ANLLPPPEPK ESWRRIMDEL
SVISCDVYRG YVRENKDFVP YFRSATPEQE LGKLPLGSRP AKRRPTGGVE SLRAIPWIFA
WTQNRLMLPA WLGAGTALQK VVEDGKQSEL EAMCRDWPFF STRLGMLEMV FAKADLWLAE
YYDQRLVDKA LWPLGKELRN LQEEDIKVVL AIANDSHLMA DLPWIAESIQ LRNIYTDPLN
VLQAELLHRS RQAEKEGQEP DPRVEQALMV TIAGIAAGMR NTG
Length

883

Mol. Wt

99.065 kDa

pI

5.6 (calculated)

Extinction coefficient

138,770 - 139,770 (calc based on 23 Y, 19 W, and 8 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

Domain

280..883

PF00311 Phosphoenolpyruvate carboxylase

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=ppc 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:16131794

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948457

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012950

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P00864

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10756

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10756

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948457

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000747

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0749

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

8.51E+02

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

14.585+/-0.258

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.180497925

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

2530

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

4441

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

2495

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)

ppc

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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_000913:4151101..4151141 source=MG1655 flip=1 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:b3956 (EcoliWiki Page)

NCBI GEO profiles for ppc

microarray

GenExpDB:b3956 (EcoliWiki Page)

Summary of data for ppc 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 ppc Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10756

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0749

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3956

EcoGene

EcoGene:EG10756

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000747

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012950

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

Arabidopsis thaliana

  • AT1G68750 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0187592 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • P29194 (score: 1.000; bootstrap: 100%)
  • P51059 (score: 0.963)
  • Q69LW4 (score: 0.928)
  • O82072 (score: 0.910)
  • Q8H4V1 (score: 0.904)
  • Q84XH0 (score: 0.893)
  • P29193 (score: 0.820)
  • Q9FYX8 (score: 0.797)
  • Q6EUD7 (score: 0.797)
  • Q9SAZ6 (score: 0.788)
  • P29195 (score: 0.788)
  • Q6RUV4 (score: 0.784)
  • Q84MZ3 (score: 0.772)
  • Q5JLS6 (score: 0.753)
  • Q8S2Z8 (score: 0.706)
  • Q43267 (score: 0.685)
  • Q84KR7 (score: 0.683)
  • P04711 (score: 0.682)
  • Q9FQ80 (score: 0.674)
  • Q5QNA5 (score: 0.665)
  • Q8L6C3 (score: 0.649)
  • Q9FS96 (score: 0.649)
  • Q8H1X3 (score: 0.644)
  • P15804 (score: 0.635)
  • Q5D5T4 (score: 0.216)
  • Q657S3 (score: 0.065)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000027913 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

PPC

From SHIGELLACYC

E. coli O157

PPC

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:51621

Pfam (EcoliWiki Page)

PF00311 Phosphoenolpyruvate carboxylase

EcoCyc

EcoCyc:EG10756

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10756

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000747

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0749

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012950

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 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).

Categories

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