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Protein

Protein-arginine deiminase type-2

Gene

PADI2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the deimination of arginine residues of proteins.By similarity

Catalytic activityi

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

Cofactori

Ca2+By similarity

GO - Molecular functioni

  • calcium ion binding Source: InterPro
  • estrogen receptor binding Source: UniProtKB
  • protein-arginine deiminase activity Source: UniProtKB

GO - Biological processi

  • chromatin-mediated maintenance of transcription Source: UniProtKB
  • histone H3-R26 citrullination Source: UniProtKB
  • intracellular estrogen receptor signaling pathway Source: UniProtKB
  • negative regulation of chemokine-mediated signaling pathway Source: UniProtKB
  • negative regulation of lymphocyte chemotaxis Source: UniProtKB
  • protein citrullination Source: UniProtKB
  • regulation of chromatin disassembly Source: UniProtKB
  • substantia nigra development Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Calcium

Enzyme and pathway databases

BioCyciMetaCyc:HS04094-MONOMER.
BRENDAi3.5.3.15. 2681.

Names & Taxonomyi

Protein namesi
Recommended name:
Protein-arginine deiminase type-2 (EC:3.5.3.15)
Alternative name(s):
PAD-H19
Peptidylarginine deiminase II
Protein-arginine deiminase type II
Gene namesi
Name:PADI2
Synonyms:KIAA0994, PDI2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:18341. PADI2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • transcriptionally active chromatin Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA32900.

Chemistry

DrugBankiDB00155. L-Citrulline.

Polymorphism and mutation databases

BioMutaiPADI2.
DMDMi7531171.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 665665Protein-arginine deiminase type-2PRO_0000220026Add
BLAST

Proteomic databases

MaxQBiQ9Y2J8.
PaxDbiQ9Y2J8.
PRIDEiQ9Y2J8.

PTM databases

PhosphoSiteiQ9Y2J8.

Expressioni

Gene expression databases

BgeeiQ9Y2J8.
CleanExiHS_PADI2.
ExpressionAtlasiQ9Y2J8. baseline and differential.
GenevisibleiQ9Y2J8. HS.

Organism-specific databases

HPAiHPA047735.

Interactioni

Protein-protein interaction databases

BioGridi116404. 1 interaction.
IntActiQ9Y2J8. 1 interaction.
STRINGi9606.ENSP00000364635.

Structurei

Secondary structure

1
665
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Beta strandi11 – 133Combined sources
Beta strandi15 – 206Combined sources
Beta strandi24 – 274Combined sources
Beta strandi30 – 334Combined sources
Beta strandi39 – 446Combined sources
Beta strandi49 – 546Combined sources
Beta strandi57 – 615Combined sources
Beta strandi75 – 806Combined sources
Beta strandi86 – 883Combined sources
Beta strandi91 – 988Combined sources
Beta strandi106 – 12116Combined sources
Beta strandi126 – 1294Combined sources
Turni135 – 1384Combined sources
Beta strandi149 – 1513Combined sources
Beta strandi162 – 1643Combined sources
Helixi166 – 1683Combined sources
Helixi175 – 1784Combined sources
Beta strandi181 – 19313Combined sources
Beta strandi198 – 2036Combined sources
Helixi207 – 2104Combined sources
Beta strandi212 – 2165Combined sources
Helixi220 – 2223Combined sources
Beta strandi226 – 2316Combined sources
Beta strandi236 – 2394Combined sources
Beta strandi243 – 25412Combined sources
Beta strandi264 – 27411Combined sources
Beta strandi283 – 29412Combined sources
Beta strandi306 – 3127Combined sources
Helixi318 – 32912Combined sources
Beta strandi334 – 3385Combined sources
Helixi340 – 3434Combined sources
Helixi348 – 3514Combined sources
Beta strandi353 – 3608Combined sources
Beta strandi363 – 3708Combined sources
Beta strandi375 – 3773Combined sources
Helixi383 – 3864Combined sources
Beta strandi391 – 3944Combined sources
Beta strandi398 – 4003Combined sources
Helixi404 – 4063Combined sources
Helixi408 – 4103Combined sources
Beta strandi411 – 4133Combined sources
Beta strandi417 – 4193Combined sources
Beta strandi422 – 4243Combined sources
Beta strandi429 – 4335Combined sources
Turni436 – 4394Combined sources
Helixi445 – 4539Combined sources
Beta strandi460 – 4634Combined sources
Beta strandi467 – 4693Combined sources
Helixi472 – 4743Combined sources
Beta strandi476 – 4805Combined sources
Beta strandi487 – 4937Combined sources
Helixi494 – 50613Combined sources
Turni507 – 5115Combined sources
Beta strandi513 – 5153Combined sources
Turni519 – 5213Combined sources
Helixi522 – 5243Combined sources
Helixi528 – 5325Combined sources
Helixi535 – 55925Combined sources
Helixi563 – 5653Combined sources
Beta strandi566 – 5705Combined sources
Beta strandi573 – 5753Combined sources
Beta strandi581 – 5855Combined sources
Beta strandi592 – 5943Combined sources
Beta strandi597 – 6015Combined sources
Helixi613 – 62210Combined sources
Helixi623 – 6253Combined sources
Beta strandi628 – 6325Combined sources
Helixi636 – 6383Combined sources
Beta strandi648 – 6536Combined sources
Helixi660 – 6623Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4N20X-ray1.66A1-665[»]
4N22X-ray1.89A1-665[»]
4N24X-ray1.97A1-665[»]
4N25X-ray1.93A1-665[»]
4N26X-ray1.94A1-665[»]
4N28X-ray1.88A1-665[»]
4N2AX-ray1.70A1-665[»]
4N2BX-ray1.69A1-665[»]
4N2CX-ray3.02A1-665[»]
4N2DX-ray2.00A1-665[»]
4N2EX-ray1.86A1-665[»]
4N2FX-ray1.80A1-665[»]
4N2GX-ray1.85A1-665[»]
4N2HX-ray1.81A1-665[»]
4N2IX-ray1.90A1-665[»]
4N2KX-ray1.57A1-665[»]
4N2LX-ray2.10A1-665[»]
4N2MX-ray1.60A1-665[»]
4N2NX-ray1.80A1-665[»]
ProteinModelPortaliQ9Y2J8.
SMRiQ9Y2J8. Positions 3-665.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the protein arginine deiminase family.Curated

Phylogenomic databases

eggNOGiNOG42085.
GeneTreeiENSGT00390000008680.
HOGENOMiHOG000220908.
HOVERGENiHBG053016.
InParanoidiQ9Y2J8.
KOiK01481.
OMAiCLETHVR.
OrthoDBiEOG7P5T09.
PhylomeDBiQ9Y2J8.
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.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y2J8-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MLRERTVRLQ YGSRVEAVYV LGTYLWTDVY SAAPAGAQTF SLKHSEHVWV
60 70 80 90 100
EVVRDGEAEE VATNGKQRWL LSPSTTLRVT MSQASTEASS DKVTVNYYDE
110 120 130 140 150
EGSIPIDQAG LFLTAIEISL DVDADRDGVV EKNNPKKASW TWGPEGQGAI
160 170 180 190 200
LLVNCDRETP WLPKEDCRDE KVYSKEDLKD MSQMILRTKG PDRLPAGYEI
210 220 230 240 250
VLYISMSDSD KVGVFYVENP FFGQRYIHIL GRRKLYHVVK YTGGSAELLF
260 270 280 290 300
FVEGLCFPDE GFSGLVSIHV SLLEYMAQDI PLTPIFTDTV IFRIAPWIMT
310 320 330 340 350
PNILPPVSVF VCCMKDNYLF LKEVKNLVEK TNCELKVCFQ YLNRGDRWIQ
360 370 380 390 400
DEIEFGYIEA PHKGFPVVLD SPRDGNLKDF PVKELLGPDF GYVTREPLFE
410 420 430 440 450
SVTSLDSFGN LEVSPPVTVN GKTYPLGRIL IGSSFPLSGG RRMTKVVRDF
460 470 480 490 500
LKAQQVQAPV ELYSDWLTVG HVDEFMSFVP IPGTKKFLLL MASTSACYKL
510 520 530 540 550
FREKQKDGHG EAIMFKGLGG MSSKRITINK ILSNESLVQE NLYFQRCLDW
560 570 580 590 600
NRDILKKELG LTEQDIIDLP ALFKMDEDHR ARAFFPNMVN MIVLDKDLGI
610 620 630 640 650
PKPFGPQVEE ECCLEMHVRG LLEPLGLECT FIDDISAYHK FLGEVHCGTN
660
VRRKPFTFKW WHMVP
Length:665
Mass (Da):75,564
Last modified:May 30, 2000 - v2
Checksum:i8D417A87A02D6839
GO
Isoform 2 (identifier: Q9Y2J8-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     438-665: Missing.

Note: No experimental confirmation available.
Show »
Length:437
Mass (Da):49,310
Checksum:i912B81FDA3DAC1A4
GO

Sequence cautioni

The sequence BAA76838.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti661 – 6611W → L in BAA82557 (PubMed:12392711).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei438 – 665228Missing in isoform 2. 1 PublicationVSP_056385Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB030176 mRNA. Translation: BAA82557.1.
AJ549502 Genomic DNA. Translation: CAE47740.1.
AB023211 mRNA. Translation: BAA76838.1. Different initiation.
AL049569 Genomic DNA. Translation: CAB96821.1.
BC009701 mRNA. Translation: AAH09701.1.
CCDSiCCDS177.1. [Q9Y2J8-1]
RefSeqiNP_031391.2. NM_007365.2. [Q9Y2J8-1]
UniGeneiHs.33455.

Genome annotation databases

EnsembliENST00000375481; ENSP00000364630; ENSG00000117115. [Q9Y2J8-2]
ENST00000375486; ENSP00000364635; ENSG00000117115. [Q9Y2J8-1]
GeneIDi11240.
KEGGihsa:11240.
UCSCiuc001baf.3. human. [Q9Y2J8-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB030176 mRNA. Translation: BAA82557.1.
AJ549502 Genomic DNA. Translation: CAE47740.1.
AB023211 mRNA. Translation: BAA76838.1. Different initiation.
AL049569 Genomic DNA. Translation: CAB96821.1.
BC009701 mRNA. Translation: AAH09701.1.
CCDSiCCDS177.1. [Q9Y2J8-1]
RefSeqiNP_031391.2. NM_007365.2. [Q9Y2J8-1]
UniGeneiHs.33455.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4N20X-ray1.66A1-665[»]
4N22X-ray1.89A1-665[»]
4N24X-ray1.97A1-665[»]
4N25X-ray1.93A1-665[»]
4N26X-ray1.94A1-665[»]
4N28X-ray1.88A1-665[»]
4N2AX-ray1.70A1-665[»]
4N2BX-ray1.69A1-665[»]
4N2CX-ray3.02A1-665[»]
4N2DX-ray2.00A1-665[»]
4N2EX-ray1.86A1-665[»]
4N2FX-ray1.80A1-665[»]
4N2GX-ray1.85A1-665[»]
4N2HX-ray1.81A1-665[»]
4N2IX-ray1.90A1-665[»]
4N2KX-ray1.57A1-665[»]
4N2LX-ray2.10A1-665[»]
4N2MX-ray1.60A1-665[»]
4N2NX-ray1.80A1-665[»]
ProteinModelPortaliQ9Y2J8.
SMRiQ9Y2J8. Positions 3-665.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116404. 1 interaction.
IntActiQ9Y2J8. 1 interaction.
STRINGi9606.ENSP00000364635.

Chemistry

BindingDBiQ9Y2J8.
ChEMBLiCHEMBL1909487.
DrugBankiDB00155. L-Citrulline.

PTM databases

PhosphoSiteiQ9Y2J8.

Polymorphism and mutation databases

BioMutaiPADI2.
DMDMi7531171.

Proteomic databases

MaxQBiQ9Y2J8.
PaxDbiQ9Y2J8.
PRIDEiQ9Y2J8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000375481; ENSP00000364630; ENSG00000117115. [Q9Y2J8-2]
ENST00000375486; ENSP00000364635; ENSG00000117115. [Q9Y2J8-1]
GeneIDi11240.
KEGGihsa:11240.
UCSCiuc001baf.3. human. [Q9Y2J8-1]

Organism-specific databases

CTDi11240.
GeneCardsiGC01M017393.
HGNCiHGNC:18341. PADI2.
HPAiHPA047735.
MIMi607935. gene.
neXtProtiNX_Q9Y2J8.
PharmGKBiPA32900.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG42085.
GeneTreeiENSGT00390000008680.
HOGENOMiHOG000220908.
HOVERGENiHBG053016.
InParanoidiQ9Y2J8.
KOiK01481.
OMAiCLETHVR.
OrthoDBiEOG7P5T09.
PhylomeDBiQ9Y2J8.
TreeFamiTF331952.

Enzyme and pathway databases

BioCyciMetaCyc:HS04094-MONOMER.
BRENDAi3.5.3.15. 2681.

Miscellaneous databases

ChiTaRSiPADI2. human.
GeneWikiiPADI2.
GenomeRNAii11240.
NextBioi42778.
PROiQ9Y2J8.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y2J8.
CleanExiHS_PADI2.
ExpressionAtlasiQ9Y2J8. baseline and differential.
GenevisibleiQ9Y2J8. HS.

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

« Hide 'large scale' publications
  1. "Human peptidylarginine deiminase type II: molecular cloning, gene organization, and expression in human skin."
    Ishigami A., Ohsawa T., Asaga H., Akiyama K., Kuramoto M., Maruyama N.
    Arch. Biochem. Biophys. 407:25-31(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION.
    Tissue: Skin.
  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].
  3. "Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Ishikawa K., Suyama M., Kikuno R., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 6:63-70(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Brain.
  4. "The DNA sequence and biological annotation of human chromosome 1."
    Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
    , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
    Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Pancreas.

Entry informationi

Entry nameiPADI2_HUMAN
AccessioniPrimary (citable) accession number: Q9Y2J8
Secondary accession number(s): Q96DA7, Q9UPN2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: June 24, 2015
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.