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Protein

Protein-arginine deiminase type-4

Gene

Padi4

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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)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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase

Keywords - Biological processi

Immunity, Innate immunity, Transcription, Transcription regulation

Keywords - Ligandi

Calcium, 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 5

Organism-specific databases

RGDi3290. Padi4.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 666666Protein-arginine deiminase type-4PRO_0000220035Add
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

PaxDbiO88807.
PRIDEiO88807.

Expressioni

Tissue specificityi

Epidermis.1 Publication

Gene expression databases

GenevisibleiO88807. RN.

Interactioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000009081.

Structurei

3D structure databases

ProteinModelPortaliO88807.
SMRiO88807. Positions 4-666.
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.
OMAiHVARSEM.
OrthoDBiEOG7P5T09.
PhylomeDBiO88807.
TreeFamiTF331952.

Family and domain databases

InterProiIPR008972. Cupredoxin.
IPR004303. PAD.
IPR013530. PAD_C.
IPR013732. PAD_N.
IPR013733. Prot_Arg_deaminase_cen_dom.
[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.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti655 – 6551K → E in BAA23523 (PubMed:9675292).Curated

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.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliO88807.
SMRiO88807. Positions 4-666.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000009081.

Proteomic databases

PaxDbiO88807.
PRIDEiO88807.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi23569.
RGDi3290. Padi4.

Phylogenomic databases

eggNOGiENOG410IF3F. Eukaryota.
ENOG410ZKF3. LUCA.
GeneTreeiENSGT00390000008680.
HOGENOMiHOG000220908.
HOVERGENiHBG053016.
InParanoidiO88807.
KOiK01481.
OMAiHVARSEM.
OrthoDBiEOG7P5T09.
PhylomeDBiO88807.
TreeFamiTF331952.

Enzyme and pathway databases

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

Miscellaneous databases

NextBioi609440.
PROiO88807.

Gene expression databases

GenevisibleiO88807. RN.

Family and domain databases

InterProiIPR008972. Cupredoxin.
IPR004303. PAD.
IPR013530. PAD_C.
IPR013732. PAD_N.
IPR013733. Prot_Arg_deaminase_cen_dom.
[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.
ProtoNetiSearch...

Publicationsi

  1. "Molecular cloning of two novel types of peptidylarginine deiminase cDNAs from retinoic acid-treated culture of a newborn rat keratinocyte cell line."
    Ishigami A., Kuramoto M., Yamada M., Watanabe K., Senshu T.
    FEBS Lett. 433:113-118(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Cloning of cDNA encoding a novel isoform (type IV) of peptidylarginine deiminase from rat epidermis."
    Yamakoshi A., Ono H., Nishijyo T., Shiraiwa M., Takahara H.
    Biochim. Biophys. Acta 1386:227-232(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    Tissue: Epidermis.

Entry informationi

Entry nameiPADI4_RAT
AccessioniPrimary (citable) accession number: O88807
Secondary accession number(s): O35117
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1998
Last modified: February 17, 2016
This is version 110 of the entry and version 1 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. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.