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Protein

Protein-arginine deiminase type-4

Gene

Padi4

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

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 (By similarity).By similarity

Catalytic activityi

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

Cofactori

Ca2+By similarityNote: Binds 5 Ca2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi153Calcium 1By similarity1
Metal bindingi155Calcium 1By similarity1
Metal bindingi155Calcium 2By similarity1
Metal bindingi165Calcium 1By similarity1
Metal bindingi165Calcium 3; via carbonyl oxygenBy similarity1
Metal bindingi168Calcium 3By similarity1
Metal bindingi176Calcium 1By similarity1
Metal bindingi179Calcium 1By similarity1
Metal bindingi179Calcium 2By similarity1
Metal bindingi349Calcium 4By similarity1
Active sitei350By similarity1
Metal bindingi351Calcium 5By similarity1
Metal bindingi353Calcium 4By similarity1
Metal bindingi369Calcium 5By similarity1
Metal bindingi370Calcium 5; via carbonyl oxygenBy similarity1
Binding sitei374SubstrateBy similarity1
Metal bindingi407Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi410Calcium 4; via carbonyl oxygenBy similarity1
Metal bindingi411Calcium 4By similarity1
Active sitei471By similarity1
Active sitei473By similarity1
Active sitei648By similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Hydrolase
Biological processImmunity, Innate immunity, Transcription, Transcription regulation
LigandCalcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.5.3.15 5301
ReactomeiR-RNO-3247509 Chromatin modifying enzymes

Names & Taxonomyi

Protein namesi
Recommended name:
Protein-arginine deiminase type-4 (EC:3.5.3.15)
Alternative name(s):
PAD-R4
Peptidylarginine deiminase IV
Peptidylarginine deiminase type alpha
Protein-arginine deiminase type IV
Gene namesi
Name:Padi4
Synonyms:Pad4, Pdi4
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 5

Organism-specific databases

RGDi3290 Padi4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002200351 – 666Protein-arginine deiminase type-4Add BLAST666

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei212CitrullineBy similarity1
Modified residuei218CitrullineBy similarity1
Modified residuei372CitrullineBy similarity1
Modified residuei374CitrullineBy similarity1
Modified residuei383CitrullineBy similarity1

Post-translational modificationi

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

Keywords - PTMi

Citrullination

Proteomic databases

PaxDbiO88807
PRIDEiO88807

PTM databases

PhosphoSitePlusiO88807

Expressioni

Tissue specificityi

Epidermis.1 Publication

Gene expression databases

BgeeiENSRNOG00000006855
GenevisibleiO88807 RN

Interactioni

GO - Molecular functioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000009081

Structurei

3D structure databases

ProteinModelPortaliO88807
SMRiO88807
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the protein arginine deiminase family.Curated

Phylogenomic databases

eggNOGiENOG410IF3F Eukaryota
ENOG410ZKF3 LUCA
GeneTreeiENSGT00390000008680
HOGENOMiHOG000220908
HOVERGENiHBG053016
InParanoidiO88807
KOiK01481
OMAiRVFQATR
OrthoDBiEOG091G02QG
PhylomeDBiO88807
TreeFamiTF331952

Family and domain databases

Gene3Di2.60.40.1700, 1 hit
2.60.40.1860, 1 hit
InterProiView protein in InterPro
IPR008972 Cupredoxin
IPR004303 PAD
IPR013530 PAD_C
IPR036556 PAD_central_sf
IPR013732 PAD_N
IPR038685 PAD_N_sf
IPR013733 Prot_Arg_deaminase_cen_dom
PANTHERiPTHR10837 PTHR10837, 1 hit
PfamiView protein in Pfam
PF03068 PAD, 1 hit
PF08527 PAD_M, 1 hit
PF08526 PAD_N, 1 hit
PIRSFiPIRSF001247 Protein-arginine_deiminase, 1 hit
SUPFAMiSSF110083 SSF110083, 1 hit
SSF49503 SSF49503, 1 hit

Sequencei

Sequence statusi: Complete.

O88807-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQGAVIHVA PEEPTHAVCV VGTATPLDIR GSAPRGSTSF SITASPEVVV
60 70 80 90 100
DVIHGPPSKK STTGASKWPL DPKLEVTLQM KAASSRIDDQ KVRISYYGPK
110 120 130 140 150
TSSTQALLYL TGVELSLSAD VTRTGKAKPA PAGKDQSTWT WGPDGHGAIL
160 170 180 190 200
LVNCDKEDPK SSGMDFEDDK VLDNKDLQDM SPMTLSTKTP KDFFDKYQLV
210 220 230 240 250
LQVPKAKMNK VRVFRATRGK LPSRYKVVLG PQQFSHRLEL LGGQHSTDFY
260 270 280 290 300
VEGLAFPDAD FKGLIPLTIS LLDKSNPELP EALVFQDTVM FRVAPWIMTP
310 320 330 340 350
NTQPPQEVYV CRFSDNEDFL KSLATFTKKA KCKLTVCPEE ENQDDQWMQD
360 370 380 390 400
EMEIGYIQAP HKTLPVVFDS PRDRGLKDFP VKRVMGPNFG YVTRGLYRAE
410 420 430 440 450
VTGLDAFGNL EVSPPVTVRG KEYPLGRILI GSSGYSSSES RDMHQILQDF
460 470 480 490 500
LGAQQVQAPV RLFSDWLFVG HVDEFLSFVP ARGKQGFRLL LSSPRACYQM
510 520 530 540 550
FQELQTEGHG EASLFEGLKR KRQTISDILS SQKLRDQNAY VESCIDWNRE
560 570 580 590 600
VLKRELGLTE GDIIDIPQLF RIVGNSRGNP KAEAFFPNMV NMLVLGKHLG
610 620 630 640 650
IPKPFGPIIN GRCCLEEKVC SLLEPLGLHC TFINDFYSYH MYHGEVHCGT
660
NVRRKPFAFK WWHMVP
Length:666
Mass (Da):74,467
Last modified:November 1, 1998 - v1
Checksum:i70F23BB3B04C813B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti655K → E in BAA23523 (PubMed:9675292).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB010999 mRNA Translation: BAA32100.1
AB008803 mRNA Translation: BAA23523.1
RefSeqiNP_058923.1, NM_017227.1
UniGeneiRn.11155

Genome annotation databases

EnsembliENSRNOT00000009081; ENSRNOP00000009081; ENSRNOG00000006855
GeneIDi29512
KEGGirno:29512
UCSCiRGD:3290 rat

Similar proteinsi

Entry informationi

Entry nameiPADI4_RAT
AccessioniPrimary (citable) accession number: O88807
Secondary accession number(s): O35117
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1998
Last modified: April 25, 2018
This is version 122 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health