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PADI3 peptidyl arginine deiminase 3 [ Homo sapiens (human) ]

Gene ID: 51702, updated on 27-Nov-2024

Summary

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Official Symbol
PADI3provided by HGNC
Official Full Name
peptidyl arginine deiminase 3provided by HGNC
Primary source
HGNC:HGNC:18337
See related
Ensembl:ENSG00000142619 MIM:606755; AllianceGenome:HGNC:18337
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
PAD3; PDI3; UHS1
Summary
This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. The type III enzyme modulates hair structural proteins, such as filaggrin in the hair follicle and trichohyalin in the inner root sheath, during hair follicle formation. Together with the type I enzyme, this enzyme may also play a role in terminal differentiation of the epidermis. This gene exists in a cluster with four other paralogous genes. [provided by RefSeq, Jul 2008]
Expression
Biased expression in urinary bladder (RPKM 6.9) and esophagus (RPKM 2.4) See more
Orthologs
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Genomic context

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See PADI3 in Genome Data Viewer
Location:
1p36.13
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (17249098..17284233)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (17060334..17095464)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (17575593..17610728)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17519557-17520058 Neighboring gene long intergenic non-protein coding RNA 2783 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17536705-17537206 Neighboring gene peptidyl arginine deiminase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17585529-17586030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17586031-17586530 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:17597192-17597435 Neighboring gene NANOG hESC enhancer GRCh37_chr1:17600492-17600993 Neighboring gene microRNA 3972 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:17621951-17622120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17631014-17631874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17642404-17642961 Neighboring gene peptidyl arginine deiminase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17685053-17685772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17703685-17704186 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:17707761-17708960 Neighboring gene peptidyl arginine deiminase 6 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:17720217-17721416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:17727331-17728267

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Structural characterization of human peptidyl-arginine deiminase type III by X-ray crystallography. Rechiche O, et al. Acta Crystallogr F Struct Biol Commun, 2021 Oct 1. PMID 34605437, Free PMC Article
  2. Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design. Funabashi K, et al. Arch Biochem Biophys, 2021 Sep 15. PMID 33971157
  3. PADI3 inhibits epithelial-mesenchymal transition by targeting CKS1-induced signal transduction in colon cancer. Chai Z, et al. J Cancer Res Ther, 2024 Aug 1. PMID 39206995
  4. Crystallization and preliminary X-ray crystallographic analysis of human peptidylarginine deiminase type III. Unno M, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2012 Jun 1. PMID 22684066, Free PMC Article
  5. Variant PADI3 in Central Centrifugal Cicatricial Alopecia. Malki L, et al. N Engl J Med, 2019 Feb 28. PMID 30763140

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PADI3 inhibits epithelial-mesenchymal transition by targeting CKS1-induced signal transduction in colon cancer.
    Title: PADI3 inhibits epithelial-mesenchymal transition by targeting CKS1-induced signal transduction in colon cancer.
  2. Peptidylarginine Deiminase Inhibitor Application, Using Cl-Amidine, PAD2, PAD3 and PAD4 Isozyme-Specific Inhibitors in Pancreatic Cancer Cells, Reveals Roles for PAD2 and PAD3 in Cancer Invasion and Modulation of Extracellular Vesicle Signatures.
    Title: Peptidylarginine Deiminase Inhibitor Application, Using Cl-Amidine, PAD2, PAD3 and PAD4 Isozyme-Specific Inhibitors in Pancreatic Cancer Cells, Reveals Roles for PAD2 and PAD3 in Cancer Invasion and Modulation of Extracellular Vesicle Signatures.
  3. Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design.
    Title: Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design.
  4. Citrullination of pyruvate kinase M2 by PADI1 and PADI3 regulates glycolysis and cancer cell proliferation.
    Title: Citrullination of pyruvate kinase M2 by PADI1 and PADI3 regulates glycolysis and cancer cell proliferation.
  5. Peptidylarginine Deiminase Isozyme-Specific PAD2, PAD3 and PAD4 Inhibitors Differentially Modulate Extracellular Vesicle Signatures and Cell Invasion in Two Glioblastoma Multiforme Cell Lines.
    Title: Peptidylarginine Deiminase Isozyme-Specific PAD2, PAD3 and PAD4 Inhibitors Differentially Modulate Extracellular Vesicle Signatures and Cell Invasion in Two Glioblastoma Multiforme Cell Lines.
  6. Mutations in PADI3, which encodes a protein that is essential to proper hair-shaft formation, were associated with Central Centrifugal Cicatricial Alopecia.
    Title: Variant PADI3 in Central Centrifugal Cicatricial Alopecia.
  7. The two enzymes PADI3 and TGM3, responsible for posttranslational protein modifications, and their target structural protein TCHH are all involved in hair shaft formation.
    Title: Mutations in Three Genes Encoding Proteins Involved in Hair Shaft Formation Cause Uncombable Hair Syndrome.
  8. Identify acefylline as an activator of peptidylarginine deiminase 1 and 3 in the epidermis, resulting in filaggrin deimination.
    Title: Acefylline activates filaggrin deimination by peptidylarginine deiminases in the upper epidermis.
  9. We identified the presence of PADI3 mRNA expression in synovial tissue and PADI2 and PADI4 mRNA expressions in fibroblast-like synoviocytes from patients with rheumatoid arthritis.
    Title: The amount of citrullinated proteins in synovial tissue is related to serum anti-cyclic citrullinated peptide (anti-CCP) antibody levels.
  10. The prevalence and extent of ILD was markedly higher among RA patients with anti-PAD3/4 cross-reactive antibodies, even after accounting for relevant confounders, particularly among ever smokers.
    Title: Association of cross-reactive antibodies targeting peptidyl-arginine deiminase 3 and 4 with rheumatoid arthritis-associated interstitial lung disease.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Uncombable hair syndrome 1
MedGen: C4551573 OMIM: 191480 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC126307, MGC126308

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables histone H1R54 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H2AR3 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3R17 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3R2 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3R26 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3R8 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H4R3 arginine deiminase activity IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-arginine deiminase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-arginine deiminase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
protein-arginine deiminase type-3
Names
peptidyl arginine deiminase, type III
peptidylarginine deiminase III
protein-arginine deiminase type III
NP_057317.2
XP_011539873.1
XP_011539874.1
XP_016856952.1
XP_054187652.1
XP_054187653.1
XP_054187654.1
XP_054192965.1
XP_054192966.1
XP_054192967.1

NCBI Reference Sequences (RefSeq)

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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_052788.1 RefSeqGene

    Range
    5020..40155
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_016233.2 → NP_057317.2  protein-arginine deiminase type-3

    See identical proteins and their annotated locations for NP_057317.2

    Status: REVIEWED

    Source sequence(s)
    AL590644, BC041592
    Consensus CDS
    CCDS179.1
    UniProtKB/Swiss-Prot
    Q58EY7, Q70SX5, Q9ULW8
    Related
    ENSP00000364609.3, ENST00000375460.3
    Conserved Domains (3) summary
    pfam03068
    Location:286 → 661
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 113
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:115 → 273
    PAD_M; Protein-arginine deiminase (PAD) middle 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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    17249098..17284233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541572.3 → XP_011539874.1  protein-arginine deiminase type-3 isoform X3

    See identical proteins and their annotated locations for XP_011539874.1

    Conserved Domains (3) summary
    pfam03068
    Location:286 → 385
    PAD; Protein-arginine deiminase (PAD)
    pfam08526
    Location:1 → 113
    PAD_N; Protein-arginine deiminase (PAD) N-terminal domain
    pfam08527
    Location:115 → 272
    PAD_M; Protein-arginine deiminase (PAD) middle domain

  2. XM_011541571.3 → XP_011539873.1  protein-arginine deiminase type-3 isoform X1

    See identical proteins and their annotated locations for XP_011539873.1

    Conserved Domains (3) summary
    pfam03068
    Location:248 → 623
    PAD; Protein-arginine deiminase (PAD)
    pfam08527
    Location:77 → 234
    PAD_M; Protein-arginine deiminase (PAD) middle domain
    cl19115
    Location:1 → 76
    Cupredoxin; Cupredoxin superfamily

  3. XM_017001463.2 → XP_016856952.1  protein-arginine deiminase type-3 isoform X2

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332688.1 Reference GRCh38.p14 PATCHES

    Range
    91612..126747
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331679.1 → XP_054187654.1  protein-arginine deiminase type-3 isoform X3

  2. XM_054331677.1 → XP_054187652.1  protein-arginine deiminase type-3 isoform X1

  3. XM_054331678.1 → XP_054187653.1  protein-arginine deiminase type-3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    17060334..17095464
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336992.1 → XP_054192967.1  protein-arginine deiminase type-3 isoform X3

  2. XM_054336990.1 → XP_054192965.1  protein-arginine deiminase type-3 isoform X1

  3. XM_054336991.1 → XP_054192966.1  protein-arginine deiminase type-3 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9ULW8.2 GenPept UniProtKB/Swiss-Prot:Q9ULW8

Gene LinkOut

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