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Q9Z183

- PADI4_MOUSE

UniProt

Q9Z183 - PADI4_MOUSE

Protein

Protein-arginine deiminase type-4

Gene

Padi4

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 106 (01 Oct 2014)
      Sequence version 3 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Catalyzes the citrullination/deimination of arginine residues of proteins such as histones, thereby playing a key role in histone code and regulation of stem cell maintenance. Citrullinates histone H1 at 'Arg-54' (to form H1R54ci), histone H3 at 'Arg-2', 'Arg-8', 'Arg-17' and/or 'Arg-26' (to form H3R2ci, H3R8ci, H3R17ci, H3R26ci, respectively) and histone H4 at 'Arg-3' (to form H4R3ci). Acts as a key regulator of stem cell maintenance by mediating citrullination of histone H1: citrullination of 'Arg-54' of histone H1 (H1R54ci) results in H1 displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance. Promotes profound chromatin decondensation during the innate immune response to infection in neutrophils by mediating formation of H1R54ci. Citrullination of histone H3 prevents their methylation by CARM1 and HRMT1L2/PRMT1 and represses transcription. Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1.4 Publications

    Catalytic activityi

    Protein L-arginine + H2O = protein L-citrulline + NH3.

    Cofactori

    Binds 5 calcium ions per subunit.By similarity

    Enzyme regulationi

    Strongly Inhibited by F-amidine and N-alpha-benzoyl-N5-(2-chloro-1-iminoethyl)-L-ornithine amide (Cl-amidine). These inhibitors are however not specific to PADI4 and also inhibit other members of the family.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi153 – 1531Calcium 1By similarity
    Metal bindingi155 – 1551Calcium 1By similarity
    Metal bindingi155 – 1551Calcium 2By similarity
    Metal bindingi165 – 1651Calcium 1By similarity
    Metal bindingi165 – 1651Calcium 3; via carbonyl oxygenBy similarity
    Metal bindingi168 – 1681Calcium 3By similarity
    Metal bindingi176 – 1761Calcium 1By similarity
    Metal bindingi179 – 1791Calcium 1By similarity
    Metal bindingi179 – 1791Calcium 2By similarity
    Metal bindingi349 – 3491Calcium 4By similarity
    Active sitei350 – 3501By similarity
    Metal bindingi351 – 3511Calcium 5By similarity
    Metal bindingi353 – 3531Calcium 4By similarity
    Metal bindingi369 – 3691Calcium 5By similarity
    Metal bindingi370 – 3701Calcium 5; via carbonyl oxygenBy similarity
    Binding sitei374 – 3741SubstrateBy similarity
    Metal bindingi407 – 4071Calcium 4; via carbonyl oxygenBy similarity
    Metal bindingi410 – 4101Calcium 4; via carbonyl oxygenBy similarity
    Metal bindingi411 – 4111Calcium 4By similarity
    Active sitei471 – 4711By similarity
    Active sitei473 – 4731By similarity
    Active sitei648 – 6481By similarity

    GO - Molecular functioni

    1. arginine deiminase activity Source: Ensembl
    2. calcium ion binding Source: UniProtKB
    3. protein-arginine deiminase activity Source: UniProtKB

    GO - Biological processi

    1. chromatin modification Source: UniProtKB
    2. chromatin remodeling Source: UniProtKB
    3. histone citrullination Source: UniProtKB
    4. histone H3-R26 citrullination Source: UniProtKB
    5. innate immune response Source: UniProtKB-KW
    6. nucleosome assembly Source: UniProtKB
    7. regulation of transcription, DNA-templated Source: UniProtKB-KW
    8. stem cell maintenance Source: UniProtKB
    9. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chromatin regulator, Hydrolase

    Keywords - Biological processi

    Immunity, Innate immunity, Transcription, Transcription regulation

    Keywords - Ligandi

    Calcium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein-arginine deiminase type-4 (EC:3.5.3.15)
    Alternative name(s):
    Peptidylarginine deiminase IV
    Protein-arginine deiminase type IV
    Gene namesi
    Name:Padi4
    Synonyms:Pdi4
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 4

    Organism-specific databases

    MGIiMGI:1338898. Padi4.

    Subcellular locationi

    Cytoplasm By similarity. Nucleus By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    2. nucleus Source: UniProtKB

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Mice survive to adulthood and do not display detectable physical abnormality. However, mice were born at a rate lower than predicted by the Mendelian ratio and display defects in innate immune response. Mice are more susceptible to bacterial infection: neutrophils cannot form neutrophil extracellular traps (NETs) after stimulation with chemokines or incubation with bacteria, and are deficient in bacterial killing by NETs. Less than 10% of deficient mice produce a thrombus 48 hours after inferior vena cava stenosis whereas 90% of wild-type mice do.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 666666Protein-arginine deiminase type-4PRO_0000220034Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei212 – 2121CitrullineBy similarity
    Modified residuei218 – 2181CitrullineBy similarity
    Modified residuei372 – 3721CitrullineBy similarity
    Modified residuei374 – 3741CitrullineBy similarity
    Modified residuei383 – 3831CitrullineBy similarity

    Post-translational modificationi

    Autocitrullination at Arg-372 and Arg-374 inactivates the enzyme.By similarity

    Keywords - PTMi

    Citrullination

    Proteomic databases

    MaxQBiQ9Z183.
    PRIDEiQ9Z183.

    PTM databases

    PhosphoSiteiQ9Z183.

    Expressioni

    Tissue specificityi

    Expressed in pluripotent embryonic stem and induced pluripotent stem cells but not multipotent neural stem cells.1 Publication

    Gene expression databases

    BgeeiQ9Z183.
    CleanExiMM_PADI4.
    GenevestigatoriQ9Z183.

    Interactioni

    Protein-protein interaction databases

    STRINGi10090.ENSMUSP00000026381.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Z183.
    SMRiQ9Z183. Positions 2-666.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the protein arginine deiminase family.Curated

    Phylogenomic databases

    eggNOGiNOG42085.
    GeneTreeiENSGT00390000008680.
    HOGENOMiHOG000220908.
    HOVERGENiHBG053016.
    InParanoidiA2AMU3.
    KOiK01481.
    OMAiVLGPQQP.
    OrthoDBiEOG7P5T09.
    TreeFamiTF331952.

    Family and domain databases

    InterProiIPR008972. Cupredoxin.
    IPR004303. PAD.
    IPR013530. PAD_C.
    IPR013732. PAD_N.
    IPR013733. Prot_Arg_deaminase_cen_dom.
    IPR016296. Protein-arginine_deiminase_sub.
    [Graphical view]
    PANTHERiPTHR10837. PTHR10837. 1 hit.
    PfamiPF03068. PAD. 1 hit.
    PF08527. PAD_M. 1 hit.
    PF08526. PAD_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001247. Protein-arginine_deiminase. 1 hit.
    SUPFAMiSSF110083. SSF110083. 1 hit.
    SSF49503. SSF49503. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9Z183-1 [UniParc]FASTAAdd to Basket

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    MAQGAVIHVA PEQPTHAVCV VGTATPLDVR GSAPKGYTTF GITASPGVIV    50
    DVIHGPPVKK STMGASKWPL DPELEVTLQV KAASSRTDDE KVRVSYYGPK 100
    TSPVQALIYI TGVELSLSAD VTRTGRVKPA QAGKDQSTWT WGPGGRGAIL 150
    LVNCDKEDPQ ASGMDFEDDK ILDNKDLQDM SPMTLSTKTP KDFFEKYQLV 200
    LEVPKAKMNR VRVFRATRGK LPSRYKVALG PQQFSYCLEL PGGQHSTDFY 250
    VEGLAFPDAD FKGLIPLTIS LLDKSNPELP EALVFQDSVT FRVAPWIMTP 300
    NTQPPQEVYV CRVSDNEDFL KSLATLTKKA KCKLTVCPEE ENIDDQWMQD 350
    EMEIGYIQAP HKTLPVVFDS PRDRGLKDFP VKRVMGPNFG YVTRKLYMSE 400
    LTGLDAFGNL EVSPPVTVRG KEYPLGRILI GNSGYSSSES RDMHQALQDF 450
    LSAQQVQAPV RLFSDWLFVG HVDEFLSFVP ARDKQGFRLL LSSPRACYQL 500
    FQELQSQGHG EATLFEGLKR KRQTINEILS NKKLRDQNAY VESCIDWNRA 550
    VLKRELGLAE GDIIDIPQLF KLAGNSRGNS KAQAFFPNMV NMLVLGKYLG 600
    IPKPFGPIID GHCCLEEEVR SHLEPLGLHC TFINDFYTYH VYNGEVHCGT 650
    NVRRKPFTFK WWHMVP 666
    Length:666
    Mass (Da):74,415
    Last modified:July 27, 2011 - v3
    Checksum:iF25B7A7B69285C32
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti41 – 411G → S in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti90 – 901E → Q in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti99 – 991P → L in BAD16627. (PubMed:15087120)Curated
    Sequence conflicti131 – 1311Q → P in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti210 – 2101R → K in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti222 – 2221P → L in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti481 – 4811A → V in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti573 – 5731A → V in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti612 – 6121H → R in BAA34246. (PubMed:10092850)Curated
    Sequence conflicti655 – 6562KP → T in BAD16627. (PubMed:15087120)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB013850 mRNA. Translation: BAA34246.1.
    AB121692 Genomic DNA. Translation: BAD16627.1.
    AL807805 Genomic DNA. Translation: CAM25732.1.
    CCDSiCCDS18854.1.
    RefSeqiNP_035191.2. NM_011061.2.
    UniGeneiMm.250358.

    Genome annotation databases

    EnsembliENSMUST00000026381; ENSMUSP00000026381; ENSMUSG00000025330.
    GeneIDi18602.
    KEGGimmu:18602.
    UCSCiuc008vne.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB013850 mRNA. Translation: BAA34246.1 .
    AB121692 Genomic DNA. Translation: BAD16627.1 .
    AL807805 Genomic DNA. Translation: CAM25732.1 .
    CCDSi CCDS18854.1.
    RefSeqi NP_035191.2. NM_011061.2.
    UniGenei Mm.250358.

    3D structure databases

    ProteinModelPortali Q9Z183.
    SMRi Q9Z183. Positions 2-666.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10090.ENSMUSP00000026381.

    PTM databases

    PhosphoSitei Q9Z183.

    Proteomic databases

    MaxQBi Q9Z183.
    PRIDEi Q9Z183.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000026381 ; ENSMUSP00000026381 ; ENSMUSG00000025330 .
    GeneIDi 18602.
    KEGGi mmu:18602.
    UCSCi uc008vne.2. mouse.

    Organism-specific databases

    CTDi 23569.
    MGIi MGI:1338898. Padi4.

    Phylogenomic databases

    eggNOGi NOG42085.
    GeneTreei ENSGT00390000008680.
    HOGENOMi HOG000220908.
    HOVERGENi HBG053016.
    InParanoidi A2AMU3.
    KOi K01481.
    OMAi VLGPQQP.
    OrthoDBi EOG7P5T09.
    TreeFami TF331952.

    Miscellaneous databases

    NextBioi 294510.
    PROi Q9Z183.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9Z183.
    CleanExi MM_PADI4.
    Genevestigatori Q9Z183.

    Family and domain databases

    InterProi IPR008972. Cupredoxin.
    IPR004303. PAD.
    IPR013530. PAD_C.
    IPR013732. PAD_N.
    IPR013733. Prot_Arg_deaminase_cen_dom.
    IPR016296. Protein-arginine_deiminase_sub.
    [Graphical view ]
    PANTHERi PTHR10837. PTHR10837. 1 hit.
    Pfami PF03068. PAD. 1 hit.
    PF08527. PAD_M. 1 hit.
    PF08526. PAD_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF001247. Protein-arginine_deiminase. 1 hit.
    SUPFAMi SSF110083. SSF110083. 1 hit.
    SSF49503. SSF49503. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Molecular cloning of cDNAs of mouse peptidylarginine deiminase type I, type III and type IV, and the expression pattern of type I in mouse."
      Rusd A.A., Ikejiri Y., Ono H., Yonekawa T., Shiraiwa M., Kawada A., Takahara H.
      Eur. J. Biochem. 259:660-669(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Tissue: Epidermis.
    2. "Comparative analysis of the mouse and human peptidylarginine deiminase gene clusters reveals highly conserved non-coding segments and a new human gene, PADI6."
      Chavanas S., Mechin M.-C., Takahara H., Kawada A., Nachat R., Serre G., Simon M.
      Gene 330:19-27(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 129/SvJ.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: C57BL/6J.
    4. Cited for: FUNCTION.
    5. "PAD4 is essential for antibacterial innate immunity mediated by neutrophil extracellular traps."
      Li P., Li M., Lindberg M.R., Kennett M.J., Xiong N., Wang Y.
      J. Exp. Med. 207:1853-1862(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    6. "Neutrophil histone modification by peptidylarginine deiminase 4 is critical for deep vein thrombosis in mice."
      Martinod K., Demers M., Fuchs T.A., Wong S.L., Brill A., Gallant M., Hu J., Wang Y., Wagner D.D.
      Proc. Natl. Acad. Sci. U.S.A. 110:8674-8679(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    7. Cited for: FUNCTION, TISSUE SPECIFICITY, ENZYME REGULATION.

    Entry informationi

    Entry nameiPADI4_MOUSE
    AccessioniPrimary (citable) accession number: Q9Z183
    Secondary accession number(s): A2AMU3, Q75WC7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 106 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3