Human Gene PEPD (ENST00000244137.12_7) from GENCODE V47lift37
  Description: peptidase D, transcript variant 1 (from RefSeq NM_000285.4)
Gencode Transcript: ENST00000244137.12_7
Gencode Gene: ENSG00000124299.16_16
Transcript (Including UTRs)
   Position: hg19 chr19:33,877,856-34,012,697 Size: 134,842 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr19:33,878,250-34,012,666 Size: 134,417 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:33,877,856-34,012,697)mRNA (may differ from genome)Protein (493 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: PEPD_HUMAN
DESCRIPTION: RecName: Full=Xaa-Pro dipeptidase; Short=X-Pro dipeptidase; EC=3.4.13.9; AltName: Full=Imidodipeptidase; AltName: Full=Peptidase D; AltName: Full=Proline dipeptidase; Short=Prolidase;
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.
CATALYTIC ACTIVITY: Hydrolysis of Xaa-|-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.
COFACTOR: Binds 2 manganese ions per subunit.
SUBUNIT: Homodimer.
MASS SPECTROMETRY: Mass=54251.73; Method=MALDI; Range=2-493; Source=PubMed:11840567;
DISEASE: Defects in PEPD are a cause of prolidase deficiency (PD) [MIM:170100]. Prolidase deficiency is an autosomal recessive disorder associated with iminodipeptiduria. The clinical phenotype includes skin ulcers, mental retardation, recurrent infections, and a characteristic facies. These features, however are incompletely penetrant and highly variable in both age of onset and severity. There is a tight linkage between the polymorphisms of prolidase and the myotonic dystrophy trait.
SIMILARITY: Belongs to the peptidase M24B family. Eukaryotic-type prolidase subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PEPD
Diseases sorted by gene-association score: prolidase deficiency* (1702), bacterial vaginosis (31), hypermobility syndrome (16), legg-calve-perthes disease (13), sexual sadism (11), osteogenesis imperfecta, type i (8), cutaneous solitary mastocytoma (7), griscelli syndrome, type 1 (7), osteogenesis imperfecta, type iii (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 87.64 RPKM in Small Intestine - Terminal Ileum
Total median expression: 1173.61 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.9031-0.255 Picture PostScript Text
3' UTR -103.70394-0.263 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007865 - Aminopep_P_N
IPR000994 - Pept_M24_structural-domain
IPR001131 - Peptidase_M24B_aminopep-P_CS

Pfam Domains:
PF00557 - Metallopeptidase family M24
PF05195 - Aminopeptidase P, N-terminal domain

SCOP Domains:
53092 - Creatinase/prolidase N-terminal domain
55920 - Creatinase/aminopeptidase

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2IW2 - X-ray MuPIT 2OKN - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P12955
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
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  Ensembl WormBaseSGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004177 aminopeptidase activity
GO:0004181 metallocarboxypeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016787 hydrolase activity
GO:0016805 dipeptidase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
GO:0102009 proline dipeptidase activity

Biological Process:
GO:0006508 proteolysis
GO:0006520 cellular amino acid metabolic process
GO:0030574 collagen catabolic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC004305 - Homo sapiens peptidase D, mRNA (cDNA clone MGC:10905 IMAGE:3626134), complete cds.
AK225037 - Homo sapiens mRNA for Xaa-Pro dipeptidase variant, clone: adKA01621.
E02334 - cDNA sequence coding for human prolytase.
J04605 - Human prolidase (imidodipeptidase) mRNA, complete cds.
BC028295 - Homo sapiens peptidase D, mRNA (cDNA clone MGC:24893 IMAGE:4470066), complete cds.
BC015027 - Homo sapiens peptidase D, mRNA (cDNA clone MGC:9000 IMAGE:3920275), complete cds.
AK290756 - Homo sapiens cDNA FLJ75447 complete cds, highly similar to Homo sapiens peptidase D, mRNA.
AK294619 - Homo sapiens cDNA FLJ58179 complete cds, highly similar to Xaa-Pro dipeptidase (EC 3.4.13.9).
AK293126 - Homo sapiens cDNA FLJ57945 complete cds, highly similar to Xaa-Pro dipeptidase (EC 3.4.13.9).
AK291561 - Homo sapiens cDNA FLJ78243 complete cds, highly similar to Homo sapiens peptidase D, mRNA.
AK290781 - Homo sapiens cDNA FLJ78212 complete cds, highly similar to Human prolidase (imidodipeptidase) mRNA.
HM005451 - Homo sapiens clone HTL-T-138 testicular tissue protein Li 138 mRNA, complete cds.
DQ891114 - Synthetic construct clone IMAGE:100003744; FLH169444.01X; RZPDo839C0596D peptidase D (PEPD) gene, encodes complete protein.
BT006692 - Homo sapiens peptidase D mRNA, complete cds.
CR541669 - Homo sapiens full open reading frame cDNA clone RZPDo834G1027D for gene PEPD, peptidase D; complete cds, incl. stopcodon.
KJ891778 - Synthetic construct Homo sapiens clone ccsbBroadEn_01172 PEPD gene, encodes complete protein.
KJ901047 - Synthetic construct Homo sapiens clone ccsbBroadEn_10441 PEPD-like gene, encodes complete protein.
KR709341 - Synthetic construct Homo sapiens clone CCSBHm_00000717 PEPD (PEPD) mRNA, encodes complete protein.
KR709342 - Synthetic construct Homo sapiens clone CCSBHm_00000718 PEPD (PEPD) mRNA, encodes complete protein.
KR709343 - Synthetic construct Homo sapiens clone CCSBHm_00000720 PEPD (PEPD) mRNA, encodes complete protein.
KR709344 - Synthetic construct Homo sapiens clone CCSBHm_00000723 PEPD (PEPD) mRNA, encodes complete protein.
DQ894294 - Synthetic construct Homo sapiens clone IMAGE:100008754; FLH169440.01L; RZPDo839C0595D peptidase D (PEPD) gene, encodes complete protein.
CU677179 - Synthetic construct Homo sapiens gateway clone IMAGE:100020716 5' read PEPD mRNA.
AK057538 - Homo sapiens cDNA FLJ32976 fis, clone TESTI2014036, highly similar to XAA-PRO DIPEPTIDASE (EC 3.4.13.9).
JD208493 - Sequence 189517 from Patent EP1572962.
JD102393 - Sequence 83417 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K3Z1, A8K416, A8K696, A8MX47, B4DDB7, B4DGJ1, E9PCE8, ENST00000244137.1, ENST00000244137.10, ENST00000244137.11, ENST00000244137.2, ENST00000244137.3, ENST00000244137.4, ENST00000244137.5, ENST00000244137.6, ENST00000244137.7, ENST00000244137.8, ENST00000244137.9, NM_000285, P12955, PEPD , PEPD_HUMAN, PRD, Q8TBN9, Q9BT75, uc317enx.1, uc317enx.2
UCSC ID: ENST00000244137.12_7
RefSeq Accession: NM_000285.4
Protein: P12955 (aka PEPD_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PEPD:
prolidase-def (Prolidase Deficiency)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.