pepD:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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[5]

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[6]

Experiment(s):EBI-887128

Protein

pepP

PMID:15690043[6]

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

Protein

wbbJ

PMID:16606699[7]

Experiment(s):EBI-1135989

Protein

greB

PMID:16606699[7]

Experiment(s):EBI-1135989

Protein

guaC

PMID:15690043[6]

Experiment(s):EBI-893231

Protein

guaC

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

pepP

PMID:19402753[8]

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[9]

Domain

200..295

PF07687 Peptidase dimerisation domain

PMID:19920124[9]

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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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References

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

  1. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Miller, CG & Schwartz, G (1978) Peptidase-deficient mutants of Escherichia coli. J. Bacteriol. 135 603-11 PubMed
  6. ↑ 6.0 6.1 6.2 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.0 7.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.0 8.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ 9.0 9.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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