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PEPD peptidase D [ Homo sapiens (human) ]

Gene ID: 5184, updated on 3-May-2025
Official Symbol
PEPDprovided by HGNC
Official Full Name
peptidase Dprovided by HGNC
Primary source
HGNC:HGNC:8840
See related
Ensembl:ENSG00000124299 MIM:613230; AllianceGenome:HGNC:8840
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PROLIDASE
Summary
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]
Expression
Broad expression in kidney (RPKM 221.6), small intestine (RPKM 95.0) and 19 other tissues See more
Orthologs
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See PEPD in Genome Data Viewer
Location:
19q13.11
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (33386950..33521791, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35906727..36042546, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (33877856..34012697, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene aldo-keto reductase family 1 member B1 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33868709-33869402 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33880343-33881245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33883417-33884181 Neighboring gene CCAAT enhancer binding protein gamma Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33886169-33886998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33886999-33887828 Neighboring gene uncharacterized LOC124904692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33897606-33898163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33909297-33910182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33976998-33977858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33977859-33978718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33978719-33979578 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:33994022-33994738 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr19:34001184-34001982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:34011998-34012961 Neighboring gene uncharacterized LOC105372370 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:34012962-34013924 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:34024395-34024912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:34024913-34025429 Neighboring gene uncharacterized LOC100996681

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Associated conditions

Description Tests
Prolidase deficiency
MedGen: C0268532 OMIM: 170100 GeneReviews: Prolidase Deficiency
Compare labs

EBI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
EBI GWAS Catalog
A meta-analysis of genome-wide association studies for adiponectin levels in East Asians identifies a novel locus near WDR11-FGFR2.
EBI GWAS Catalog
Discovery and refinement of loci associated with lipid levels.
EBI GWAS Catalog
Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.
EBI GWAS Catalog
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.
EBI GWAS Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Clone Names

  • MGC10905

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables dipeptidase activity IEA
Inferred from Electronic Annotation
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables manganese ion binding IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables metalloaminopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
enables metallocarboxypeptidase activity TAS
Traceable Author Statement
more info
PubMed 
enables metallopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
enables peptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
 
enables proline dipeptidase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables proline dipeptidase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in amino acid metabolic process TAS
Traceable Author Statement
more info
PubMed 
involved_in collagen catabolic process IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of programmed cell death IDA
Inferred from Direct Assay
more info
PubMed 
involved_in proteolysis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in proteolysis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
 
involved_in proteolysis TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
Preferred Names
xaa-Pro dipeptidase
Names
X-Pro dipeptidase
aminoacyl-L-proline hydrolase
imidodipeptidase
proline dipeptidase
testicular tissue protein Li 138
NP_000276.2
NP_001159528.1
NP_001159529.1

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_013358.2 RefSeqGene

    Range
    5103..139944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000285.4NP_000276.2  xaa-Pro dipeptidase isoform 1

    See identical proteins and their annotated locations for NP_000276.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AW512991, BC015027
    Consensus CDS
    CCDS42544.1
    UniProtKB/Swiss-Prot
    A8K3Z1, A8K416, A8K696, A8MX47, B4DDB7, B4DGJ1, E9PCE8, P12955, Q8TBN9, Q9BT75
    UniProtKB/TrEMBL
    A0A140VJR2, J3K000
    Related
    ENSP00000244137.5, ENST00000244137.12
    Conserved Domains (2) summary
    smart01011
    Location:18155
    AMP_N; Aminopeptidase P, N-terminal domain
    cd01087
    Location:192467
    Prolidase; Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on ...
  2. NM_001166056.2NP_001159528.1  xaa-Pro dipeptidase isoform 2

    See identical proteins and their annotated locations for NP_001159528.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AK294619, AW512991
    Consensus CDS
    CCDS54245.1
    UniProtKB/TrEMBL
    A0A8V8TNF2
    Related
    ENSP00000380226.3, ENST00000397032.8
    Conserved Domains (3) summary
    smart01011
    Location:18155
    AMP_N; Aminopeptidase P, N-terminal domain
    COG0006
    Location:60435
    PepP; Xaa-Pro aminopeptidase [Amino acid transport and metabolism]
    cd01087
    Location:160426
    Prolidase; Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on ...
  3. NM_001166057.2NP_001159529.1  xaa-Pro dipeptidase isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks two alternate in-frame exons in the central coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AK293126, AW512991, BC015027, DC395475
    Consensus CDS
    CCDS54244.1
    UniProtKB/TrEMBL
    A0A8V8TLP2
    Related
    ENSP00000391890.2, ENST00000436370.7
    Conserved Domains (2) summary
    cd01087
    Location:128403
    Prolidase; Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on ...
    cl23800
    Location:1867
    Creatinase_N; Creatinase/Prolidase N-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    33386950..33521791 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    35906727..36042546 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)