pepD: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

pepD

Gene Synonym(s)

ECK0238, b0237, JW0227, pepH[1], pepH

Product Desc.

PepD[2][3];

Component of peptidase D[3]

Peptidase D, Xaa-His dipeptidase[4]

Product Synonyms(s)

aminoacyl-histidine dipeptidase (peptidase D)[1], B0237[2][1], PepH[2][1] , ECK0238, JW0227, pepH, b0237

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): pepD[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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CsgD regulon, repressed. HT_Cmplx19_Cyt: PepD+Pgm+Zwf. HT_Cmplx41_Mem: Gnd+PepD.[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

pepD

Mnemonic

Peptidase

Synonyms

ECK0238, b0237, JW0227, pepH[1], pepH

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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

5.48 minutes 

MG1655: 255716..254259
<gbrowseImage> name=NC_000913:254259..255716 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 260207..258750
<gbrowseImage> name=NC_012967:258750..260207 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 254258..255715
<gbrowseImage> name=NC_012759:254258..255715 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 255716..254259
<gbrowseImage> name=NC_007779:254259..255716 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 229820..228363
<gbrowseImage> name=NC_010473:228363..229820 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

254262

Edman degradation

PMID:2651887
PMID:7988883


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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

pepD(del) (Keio:JW0227)

deletion

deletion

PMID:16738554

Shigen

CGSC8462[5]

pepD(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

pepD(del)::kan

deletion

Biolog:respiration

unable to respire Glycyl-L-aspartate

PMID:16095938

pepD755(del)::kan

PMID:16738554

CGSC:102282


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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

JW0227

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCTGAACTGTCTCAATTATC

Primer 2:CCCTTCGCCGGAATTTCTTTCAG

8F9

Kohara Phage

Genobase

PMID:3038334

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[5]

est. P1 cotransduction: 44% [6]
Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[5]

est. P1 cotransduction: 83% [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:EG10695

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10695

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000687

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0689

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000809

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

PepD

Synonyms

aminoacyl-histidine dipeptidase (peptidase D)[1], B0237[2][1], PepH[2][1] , ECK0238, JW0227, pepH, b0237

Product description

PepD[2][3];

Component of peptidase D[3]

Peptidase D, Xaa-His dipeptidase[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:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001160

P

Seeded from EcoCyc (v14.0)

complete

GO:0006508

proteolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002933

P

Seeded from EcoCyc (v14.0)

complete

GO:0008233

peptidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0645

F

Seeded from EcoCyc (v14.0)

complete

GO:0008237

metallopeptidase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002933

F

Seeded from EcoCyc (v14.0)

complete

GO:0008237

metallopeptidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0482

F

Seeded from EcoCyc (v14.0)

complete

GO:0008270

zinc ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0862

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011650

F

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:0016805

dipeptidase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0224

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0046983

protein dimerization activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011650

F

Seeded from EcoCyc (v14.0)

complete

GO:0050897

cobalt ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0170

F

Seeded from EcoCyc (v14.0)

complete

GO:0043171

peptide catabolic process

PMID:355237

IGI: Inferred from Genetic Interaction

EcoliWiki:pepA EcoliWiki:pepB EcoliWiki:pepN EcoliWiki:pepQ


P

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 peptidase D

could be indirect

Protein

dnaK

PMID:15690043

Experiment(s):EBI-887128

Protein

pepP

PMID:15690043

Experiment(s):EBI-887128, EBI-893231

Protein

wbbJ

PMID:16606699

Experiment(s):EBI-1135989

Protein

greB

PMID:16606699

Experiment(s):EBI-1135989

Protein

guaC

PMID:15690043

Experiment(s):EBI-893231

Protein

guaC

PMID:19402753

LCMS(ID Probability):99.6

Protein

pepP

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.483963

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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 

MSELSQLSPQ PLWDIFAKIC SIPHPSYHEE QLAEYIVGWA KEKGFHVERD QVGNILIRKP
ATAGMENRKP VVLQAHLDMV PQKNNDTVHD FTKDPIQPYI DGEWVKARGT TLGADNGIGM
ASALAVLADE NVVHGPLEVL LTMTEEAGMD GAFGLQGNWL QADILINTDS EEEGEIYMGC
AGGIDFTSNL HLDREAVPAG FETFKLTLKG LKGGHSGGEI HVGLGNANKL LVRFLAGHAE
ELDLRLIDFN GGTLRNAIPR EAFATIAVAA DKVDVLKSLV NTYQEILKNE LAEKEKNLAL
LLDSVANDKA ALIAKSRDTF IRLLNATPNG VIRNSDVAKG VVETSLNVGV VTMTDNNVEI
HCLIRSLIDS GKDYVVSMLD SLGKLAGAKT EAKGAYPGWQ PDANSPVMHL VRETYQRLFN
KTPNIQIIHA GLECGLFKKP YPEMDMVSIG PTITGPHSPD EQVHIESVGH YWTLLTELLK
EIPAK
Length

485

Mol. Wt

52.916 kDa

pI

5.2 (calculated)

Extinction coefficient

47,900 - 48,400 (calc based on 10 Y, 6 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:P15288

Domain

72..481

PF01546 Peptidase family M20/M25/M40

PMID:19920124

Domain

200..295

PF07687 Peptidase dimerisation domain

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=pepD 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:16128223

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945013

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000809

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P15288

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10695

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10695

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945013

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000687

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0689

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.

Transcription of pepD is induced by phosphate limitation.[7] Induction is independent of phoB, phoR, and phoM.[7]

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

2.36E+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

165.478+/-0.65

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.02413+/-0.00439

Molecules/cell

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

by FISH

PMID:20671182

mRNA

Ecoli K-12

0.268359643

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

7408

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

1694

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

4411

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)

pepD

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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_000913:255696..255736 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:b0237 (EcoliWiki Page)

NCBI GEO profiles for pepD

microarray

GenExpDB:b0237 (EcoliWiki Page)

Summary of data for pepD 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 (255634..256035) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:G2[8]

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Notes

Accessions Related to pepD Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10695

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0689

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0237

EcoGene

EcoGene:EG10695

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000687

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000809

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

  • ENSANGP00000027878 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6V918 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

PEPD

From SHIGELLACYC

E. coli O157

PEPD

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

Pfam (EcoliWiki Page)

PF01546 Peptidase family M20/M25/M40

Panther (EcoliWiki Page)

PTHR11014:SF2

Superfamily (EcoliWiki Page)

SUPERFAMILY:53187

Pfam (EcoliWiki Page)

PF07687 Peptidase dimerisation domain

EcoCyc

EcoCyc:EG10695

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10695

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000687

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0689

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000809

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. ↑ 1.0 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 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).
  7. ↑ 7.0 7.1 Henrich, B et al. (1992) The promoter region of the Escherichia coli pepD gene: deletion analysis and control by phosphate concentration. Mol. Gen. Genet. 232 117-25 PubMed
  8. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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