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Aliases for PEPD Gene

Aliases for PEPD Gene

  • Peptidase D 2 3 4
  • Proline Dipeptidase 3 4
  • X-Pro Dipeptidase 3 4
  • Imidodipeptidase 3 4
  • PROLIDASE 3 4
  • Aminoacyl-L-Proline Hydrolase 3
  • Xaa-Pro Dipeptidase 3
  • EC 3.4.13.9 4
  • Prolidase 2
  • PRD 4

External Ids for PEPD Gene

Summaries for PEPD Gene

Entrez Gene Summary for PEPD Gene

  • This gene encodes a member of the peptidase family. The protein forms a homodimer that hydrolyzes dipeptides or tripeptides with C-terminal proline or hydroxyproline residues. The enzyme serves an important role in the recycling of proline, and may be rate limiting for the production of collagen. Mutations in this gene result in prolidase deficiency, which is characterized by the excretion of large amount of di- and tri-peptides containing proline. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

GeneCards Summary for PEPD Gene

PEPD (Peptidase D) is a Protein Coding gene. Diseases associated with PEPD include prolidase deficiency and legg-calve-perthes disease. GO annotations related to this gene include manganese ion binding and metallocarboxypeptidase activity.

UniProtKB/Swiss-Prot for PEPD Gene

  • Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen

Gene Wiki entry for PEPD Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PEPD Gene

Genomics for PEPD Gene

Genomic Location for PEPD Gene

Start:
33,386,949 bp from pter
End:
33,521,893 bp from pter
Size:
134,945 bases
Orientation:
Minus strand

Genomic View for PEPD Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PEPD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PEPD Gene

Regulatory Elements for PEPD Gene

Proteins for PEPD Gene

  • Protein details for PEPD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P12955-PEPD_HUMAN
    Recommended name:
    Xaa-Pro dipeptidase
    Protein Accession:
    P12955
    Secondary Accessions:
    • A8K3Z1
    • A8K416
    • A8K696
    • A8MX47
    • B4DDB7
    • B4DGJ1
    • E9PCE8
    • Q8TBN9
    • Q9BT75

    Protein attributes for PEPD Gene

    Size:
    493 amino acids
    Molecular mass:
    54548 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 2 manganese ions per subunit.;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PEPD Gene

    Alternative splice isoforms for PEPD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PEPD Gene

Proteomics data for PEPD Gene at MOPED

Post-translational modifications for PEPD Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PEPD Gene

Domains for PEPD Gene

Suggested Antigen Peptide Sequences for PEPD Gene

Graphical View of Domain Structure for InterPro Entry

P12955

UniProtKB/Swiss-Prot:

PEPD_HUMAN
Family:
  • Belongs to the peptidase M24B family. Eukaryotic-type prolidase subfamily.:
    • P12955
genes like me logo Genes that share domains with PEPD: view

No data available for Gene Families for PEPD Gene

Function for PEPD Gene

Molecular function for PEPD Gene

GENATLAS Biochemistry: peptidase D
UniProtKB/Swiss-Prot CatalyticActivity: Hydrolysis of Xaa- -Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on Pro- -Pro
UniProtKB/Swiss-Prot Function: Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen

Enzyme Numbers (IUBMB) for PEPD Gene

Gene Ontology (GO) - Molecular Function for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004177 aminopeptidase activity IEA --
GO:0004181 metallocarboxypeptidase activity TAS 1972707
GO:0008233 peptidase activity --
GO:0016805 dipeptidase activity IEA --
GO:0030145 manganese ion binding IEA --
genes like me logo Genes that share ontologies with PEPD: view
genes like me logo Genes that share phenotypes with PEPD: view

miRNA for PEPD Gene

miRTarBase miRNAs that target PEPD

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for PEPD Gene

Localization for PEPD Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PEPD Gene COMPARTMENTS Subcellular localization image for PEPD gene
Compartment Confidence
cytosol 2
extracellular 2
nucleus 2
endoplasmic reticulum 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PEPD: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PEPD Gene

Pathways for PEPD Gene

SuperPathways for PEPD Gene

No Data Available

Gene Ontology (GO) - Biological Process for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006520 cellular amino acid metabolic process TAS 1972707
GO:0030574 collagen catabolic process IEA --
genes like me logo Genes that share ontologies with PEPD: view

No data available for Pathways by source for PEPD Gene

Compounds for PEPD Gene

(2) HMDB Compounds for PEPD Gene

Compound Synonyms Cas Number PubMed IDs
Glycylproline
  • 1-(Aminoacetyl)proline
704-15-4
Manganese
  • manganese
7439-96-5

(38) Novoseek inferred chemical compound relationships for PEPD Gene

Compound -log(P) Hits PubMed IDs
glycylproline 93.2 8
proline 85.7 103
acetylproline 85.4 2
pepq 81.2 3
anthraquinone-2-carboxylic acid 79.7 3
genes like me logo Genes that share compounds with PEPD: view

Transcripts for PEPD Gene

Unigene Clusters for PEPD Gene

Peptidase D:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PEPD Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b
SP1: - - -
SP2: -
SP3: - - - - - -
SP4: -
SP5:
SP6:

Relevant External Links for PEPD Gene

GeneLoc Exon Structure for
PEPD
ECgene alternative splicing isoforms for
PEPD

Expression for PEPD Gene

mRNA expression in normal human tissues for PEPD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PEPD Gene

This gene is overexpressed in Kidney - Cortex (5.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PEPD Gene

SOURCE GeneReport for Unigene cluster for PEPD Gene Hs.36473

genes like me logo Genes that share expressions with PEPD: view

No data available for mRNA Expression by UniProt/SwissProt for PEPD Gene

Orthologs for PEPD Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PEPD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PEPD 35
  • 99.1 (n)
  • 98.84 (a)
PEPD 36
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PEPD 35
  • 89.32 (n)
  • 91.68 (a)
PEPD 36
  • 92 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PEPD 35
  • 89.93 (n)
  • 92.7 (a)
PEPD 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pepd 35
  • 84.18 (n)
  • 89.05 (a)
Pepd 16
Pepd 36
  • 89 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PEPD 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PEPD 36
  • 79 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pepd 35
  • 84.96 (n)
  • 89.23 (a)
chicken
(Gallus gallus)
Aves PEPD 35
  • 74.78 (n)
  • 79.11 (a)
PEPD 36
  • 78 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PEPD 36
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pepd 35
  • 71.6 (n)
  • 77.57 (a)
Str.5139 35
zebrafish
(Danio rerio)
Actinopterygii -- 35
pepd 35
  • 71.55 (n)
  • 74.43 (a)
pepd 36
  • 72 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004775 35
  • 57.49 (n)
  • 56.36 (a)
fruit fly
(Drosophila melanogaster)
Insecta Dip-C 35
  • 59.83 (n)
  • 53.35 (a)
Dip-C 36
  • 50 (a)
OneToOne
Dip-C 37
  • 50 (a)
worm
(Caenorhabditis elegans)
Secernentea K12C11.1 35
  • 56.62 (n)
  • 54.78 (a)
K12C11.1 36
  • 52 (a)
OneToOne
K12C11.1 37
  • 52 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 36
  • 27 (a)
OneToOne
-- 38
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.1123 35
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G29490 35
  • 56.88 (n)
  • 58.75 (a)
corn
(Zea mays)
Liliopsida Zm.3239 35
rice
(Oryza sativa)
Liliopsida Os.27534 35
Os02g0224400 35
  • 55.74 (n)
  • 57.2 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 48 (a)
OneToMany
CSA.8389 36
  • 50 (a)
OneToMany
Species with no ortholog for PEPD:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PEPD Gene

ENSEMBL:
Gene Tree for PEPD (if available)
TreeFam:
Gene Tree for PEPD (if available)

Paralogs for PEPD Gene

Pseudogenes.org Pseudogenes for PEPD Gene

genes like me logo Genes that share paralogs with PEPD: view

No data available for Paralogs for PEPD Gene

Variants for PEPD Gene

Sequence variations from dbSNP and Humsavar for PEPD Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs1038 -- 33,387,137(-) AATCT(C/G/T)TTTTA utr-variant-3-prime
rs3556 -- 33,387,133(-) TGTTT(C/T)ATACC utr-variant-3-prime
rs16426 -- 33,387,165(+) AAGGG(-/TAAT)TAATT utr-variant-3-prime
rs17569 -- 33,391,316(-) GTGCA(C/G/T)GACGT reference, missense, synonymous-codon
rs17570 - 33,387,931(-) CCTTC(C/T)TTAAC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PEPD Gene

Variant ID Type Subtype PubMed ID
dgv1073e1 CNV Complex 17122850
nsv911597 CNV Loss 21882294
nsv828526 CNV Loss 20364138
dgv3845n71 CNV Loss 21882294
dgv3846n71 CNV Loss 21882294
nsv470138 CNV Gain 18288195
dgv3847n71 CNV Loss 21882294
nsv522571 CNV Loss 19592680
dgv139e55 CNV Gain 17911159
nsv525549 CNV Gain 19592680
nsv828527 CNV Gain 20364138
nsv911608 CNV Loss 21882294
nsv513524 CNV Insertion 21212237
esv2469451 CNV Insertion 19546169
nsv819550 CNV Insertion 19587683
esv2718472 CNV Deletion 23290073
esv2677046 CNV Deletion 23128226

Relevant External Links for PEPD Gene

HapMap Linkage Disequilibrium report
PEPD
Human Gene Mutation Database (HGMD)
PEPD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PEPD Gene

Disorders for PEPD Gene

(1) OMIM Diseases for PEPD Gene (613230)

UniProtKB/Swiss-Prot

PEPD_HUMAN
  • Prolidase deficiency (PD) [MIM:170100]: A multisystem disorder associated with massive iminodipeptiduria and lack of or reduced prolidase activity in erythrocytes, leukocytes, or cultured fibroblasts. Clinical features include skin ulcers, developmental delay, recurrent infections, and a characteristic facies. {ECO:0000269 PubMed:12384772, ECO:0000269 PubMed:2365824, ECO:0000269 PubMed:8198124, ECO:0000269 PubMed:8900231}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for PEPD Gene

(26) Novoseek inferred disease relationships for PEPD Gene

Disease -log(P) Hits PubMed IDs
skin ulcer 73.2 10
mental retardation 61 18
bacterial vaginosis 53.8 5
leg ulcer 53.2 10
skin lesion 52.1 15

Genatlas disease for PEPD Gene

prolidase deficiency,with variable expression from no manifestation to severe progressive skin ulceration,decreased resistance to infection,impaired cognitive development

Relevant External Links for PEPD

Genetic Association Database (GAD)
PEPD
Human Genome Epidemiology (HuGE) Navigator
PEPD
genes like me logo Genes that share disorders with PEPD: view

Publications for PEPD Gene

  1. Structural organization of the gene for human prolidase (peptidase D) and demonstration of a partial gene deletion in a patient with prolidase deficiency. (PMID: 1972707) Tanoue A. … Matsuda I. (J. Biol. Chem. 1990) 2 3 23
  2. A single nucleotide change in the prolidase gene in fibroblasts from two patients with polypeptide positive prolidase deficiency. Expression of the mutant enzyme in NIH 3T3 cells. (PMID: 2365824) Tanoue A. … Matsuda I. (J. Clin. Invest. 1990) 3 4 23
  3. Mutation analysis of five new patients affected by prolidase deficiency: the lack of enzyme activity causes necrosis-like cell death in cultured fibroblasts. (PMID: 12384772) Forlino A. … Cetta G. (Hum. Genet. 2002) 3 4 23
  4. Four novel PEPD alleles causing prolidase deficiency. (PMID: 8198124) Ledoux P. … Hechtman P. (Am. J. Hum. Genet. 1994) 3 4 23
  5. Expression and molecular analysis of mutations in prolidase deficiency. (PMID: 8900231) Ledoux P. … Hechtman P. (Am. J. Hum. Genet. 1996) 3 4 23

Products for PEPD Gene

Sources for PEPD Gene

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