PADI4: Difference between revisions

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{{Infobox_gene}}
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'''Peptidyl arginine deiminase, type IV''', also known as '''PADI4''', is a human [[protein]] which in humans is encoded by the ''PADI4'' [[gene]].<ref name="pmid10488123">{{cite journal | vauthors = Nakashima K, Hagiwara T, Ishigami A, Nagata S, Asaga H, Kuramoto M, Senshu T, Yamada M | title = Molecular characterization of peptidylarginine deiminase in HL-60 cells induced by retinoic acid and 1alpha,25-dihydroxyvitamin D(3) | journal = J. Biol. Chem. | volume = 274 | issue = 39 | pages = 27786–92 |date=September 1999 | pmid = 10488123 | doi = 10.1074/jbc.274.39.27786| url = http://www.jbc.org/cgi/pmidlookup?view=long&pmid=10488123 }}</ref><ref name="entrez">{{cite web | title = Entrez Gene: PADI4 peptidyl arginine deiminase, type IV| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=23569| accessdate = }}</ref>
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==Molecular biology==
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The human gene is found on the short arm of Chromosome 1 near the [[telomere]] (1p36.13). It is located on the [[positive-sense|Watson (plus) strand]] and is 55,806 bases long. The protein is 663 amino acids long with a molecular weight of 74,095 Da.<ref name="pmid10488123"/>
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== Function ==
 
This gene is a member of a gene family which encodes enzymes responsible for the conversion of [[arginine]] to [[citrulline]] residues. This gene may play a role in [[granulocyte]] and [[macrophage]] development leading to inflammation and immune response.<ref name="entrez"/> PADI4 plays a role in the epigenetics, the deimination of arginines on histones 3 and 4 can act antagonistically to arginine methylation (Chromatin modifications and their function, Kouzarides 2007, Cell, review)
 
The protein may be found in oligomers and binds 5 [[calcium in biology|calcium]] ions per subunit. It catalyses the reaction:
 
* Protein L-arginine + H<sub>2</sub>O = protein L-citrulline + NH<sub>3</sub>


<!-- The GNF_Protein_box is automatically maintained by Protein Box Bot.  See Template:PBB_Controls to Stop updates. -->
== Subcellular and tissue distribution ==
{{GNF_Protein_box
| image = PBB_Protein_PADI4_image.jpg
| image_source = [[Protein_Data_Bank|PDB]] rendering based on 1wd8.
| PDB = {{PDB2|1wd8}}, {{PDB2|1wd9}}, {{PDB2|1wda}}, {{PDB2|2dew}}, {{PDB2|2dex}}, {{PDB2|2dey}}, {{PDB2|2dw5}}
| Name = Peptidyl arginine deiminase, type IV
| HGNCid = 18368
| Symbol = PADI4
| AltSymbols =; PAD; PADI5; PDI4; PDI5
| OMIM = 605347
| ECnumber = 
| Homologene = 7883
| MGIid = 1338898
| GeneAtlas_image1 = PBB_GE_PADI4_220001_at_tn.png
| GeneAtlas_image2 = PBB_GE_PADI4_211413_s_at_tn.png
| GeneAtlas_image3 = PBB_GE_PADI4_211412_at_tn.png
| Function = {{GNF_GO|id=GO:0004668 |text = protein-arginine deiminase activity}} {{GNF_GO|id=GO:0005509 |text = calcium ion binding}} {{GNF_GO|id=GO:0016787 |text = hydrolase activity}}
| Component = {{GNF_GO|id=GO:0005634 |text = nucleus}}
| Process = {{GNF_GO|id=GO:0006350 |text = transcription}} {{GNF_GO|id=GO:0006355 |text = regulation of transcription, DNA-dependent}} {{GNF_GO|id=GO:0006464 |text = protein modification process}} {{GNF_GO|id=GO:0016568 |text = chromatin modification}}
| Orthologs = {{GNF_Ortholog_box
    | Hs_EntrezGene = 23569
    | Hs_Ensembl = ENSG00000159339
    | Hs_RefseqProtein = NP_036519
    | Hs_RefseqmRNA = NM_012387
    | Hs_GenLoc_db = 
    | Hs_GenLoc_chr = 1
    | Hs_GenLoc_start = 17507277
    | Hs_GenLoc_end = 17563086
    | Hs_Uniprot = Q9UM07
    | Mm_EntrezGene = 18602
    | Mm_Ensembl = ENSMUSG00000025330
    | Mm_RefseqmRNA = XM_991479
    | Mm_RefseqProtein = XP_996573
    | Mm_GenLoc_db = 
    | Mm_GenLoc_chr = 4
    | Mm_GenLoc_start = 140017941
    | Mm_GenLoc_end = 140046261
    | Mm_Uniprot = Q9Z183
  }}
}}
'''Peptidyl arginine deiminase, type IV''', also known as '''PADI4''', is a human [[gene]].<ref name="entrez">{{cite web | title = Entrez Gene: PADI4 peptidyl arginine deiminase, type IV| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=23569| accessdate = }}</ref>


<!-- The PBB_Summary template is automatically maintained by Protein Box Bot.  See Template:PBB_Controls to Stop updates. -->
It is normally found in the [[cytoplasm]], [[Cell nucleus|nucleus]] and in cytoplasmic granules of [[eosinophil]]s and [[neutrophil]]s. It is not expressed in peripheral [[monocyte]]s or [[lymphocyte]]s. It is also expressed in rheumatoid arthritis synovial tissues.
{{PBB_Summary
| section_title =
| summary_text = This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine residues to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response.<ref name="entrez">{{cite web | title = Entrez Gene: PADI4 peptidyl arginine deiminase, type IV| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=23569| accessdate = }}</ref>
}}


==References==
==References==
{{reflist|2}}
{{reflist}}
 
==Further reading==
==Further reading==
{{refbegin | 2}}
{{refbegin | 2}}
{{PBB_Further_reading  
{{PBB_Further_reading  
| citations =  
| citations =  
*{{cite journal | author=Nakashima K, Hagiwara T, Ishigami A, ''et al.'' |title=Molecular characterization of peptidylarginine deiminase in HL-60 cells induced by retinoic acid and 1alpha,25-dihydroxyvitamin D(3). |journal=J. Biol. Chem. |volume=274 |issue= 39 |pages= 27786-92 |year= 1999 |pmid= 10488123 |doi=  }}
*{{cite journal   |vauthors=Nakashima K, Hagiwara T, Ishigami A, etal |title=Molecular characterization of peptidylarginine deiminase in HL-60 cells induced by retinoic acid and 1alpha,25-dihydroxyvitamin D(3). |journal=J. Biol. Chem. |volume=274 |issue= 39 |pages= 27786–92 |year= 1999 |pmid= 10488123 |doi=10.1074/jbc.274.39.27786 }}
*{{cite journal | author=Zhang QH, Ye M, Wu XY, ''et al.'' |title=Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. |journal=Genome Res. |volume=10 |issue= 10 |pages= 1546-60 |year= 2001 |pmid= 11042152 |doi=  }}
*{{cite journal   |vauthors=Zhang QH, Ye M, Wu XY, etal |title=Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. |journal=Genome Res. |volume=10 |issue= 10 |pages= 1546–60 |year= 2001 |pmid= 11042152 |doi=10.1101/gr.140200 | pmc=310934  }}
*{{cite journal | author=Asaga H, Nakashima K, Senshu T, ''et al.'' |title=Immunocytochemical localization of peptidylarginine deiminase in human eosinophils and neutrophils. |journal=J. Leukoc. Biol. |volume=70 |issue= 1 |pages= 46-51 |year= 2001 |pmid= 11435484 |doi=  }}
*{{cite journal   |vauthors=Asaga H, Nakashima K, Senshu T, etal |title=Immunocytochemical localization of peptidylarginine deiminase in human eosinophils and neutrophils. |journal=J. Leukoc. Biol. |volume=70 |issue= 1 |pages= 46–51 |year= 2001 |pmid= 11435484 |doi=  }}
*{{cite journal  | author=Nakashima K, Hagiwara T, Yamada M |title=Nuclear localization of peptidylarginine deiminase V and histone deimination in granulocytes. |journal=J. Biol. Chem. |volume=277 |issue= 51 |pages= 49562-8 |year= 2003 |pmid= 12393868 |doi= 10.1074/jbc.M208795200 }}
*{{cite journal  | vauthors=Nakashima K, Hagiwara T, Yamada M |title=Nuclear localization of peptidylarginine deiminase V and histone deimination in granulocytes. |journal=J. Biol. Chem. |volume=277 |issue= 51 |pages= 49562–8 |year= 2003 |pmid= 12393868 |doi= 10.1074/jbc.M208795200 }}
*{{cite journal | author=Strausberg RL, Feingold EA, Grouse LH, ''et al.'' |title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue= 26 |pages= 16899-903 |year= 2003 |pmid= 12477932 |doi= 10.1073/pnas.242603899 }}
*{{cite journal   |vauthors=Strausberg RL, Feingold EA, Grouse LH, etal |title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue= 26 |pages= 16899–903 |year= 2003 |pmid= 12477932 |doi= 10.1073/pnas.242603899 | pmc=139241 }}
*{{cite journal | author=Suzuki A, Yamada R, Chang X, ''et al.'' |title=Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. |journal=Nat. Genet. |volume=34 |issue= 4 |pages= 395-402 |year= 2003 |pmid= 12833157 |doi= 10.1038/ng1206 }}
*{{cite journal   |vauthors=Suzuki A, Yamada R, Chang X, etal |title=Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. |journal=Nat. Genet. |volume=34 |issue= 4 |pages= 395–402 |year= 2003 |pmid= 12833157 |doi= 10.1038/ng1206 }}
*{{cite journal | author=Barton A, Bowes J, Eyre S, ''et al.'' |title=A functional haplotype of the PADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population. |journal=Arthritis Rheum. |volume=50 |issue= 4 |pages= 1117-21 |year= 2004 |pmid= 15077293 |doi= 10.1002/art.20169 }}
*{{cite journal   |vauthors=Barton A, Bowes J, Eyre S, etal |title=A functional haplotype of the PADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population. |journal=Arthritis Rheum. |volume=50 |issue= 4 |pages= 1117–21 |year= 2004 |pmid= 15077293 |doi= 10.1002/art.20169 }}
*{{cite journal | author=Chavanas S, Méchin MC, Takahara H, ''et al.'' |title=Comparative analysis of the mouse and human peptidylarginine deiminase gene clusters reveals highly conserved non-coding segments and a new human gene, PADI6. |journal=Gene |volume=330 |issue=  |pages= 19-27 |year= 2004 |pmid= 15087120 |doi= 10.1016/j.gene.2003.12.038 }}
*{{cite journal   |vauthors=Chavanas S, Méchin MC, Takahara H, etal |title=Comparative analysis of the mouse and human peptidylarginine deiminase gene clusters reveals highly conserved non-coding segments and a new human gene, PADI6. |journal=Gene |volume=330 |issue=  |pages= 19–27 |year= 2004 |pmid= 15087120 |doi= 10.1016/j.gene.2003.12.038 }}
*{{cite journal | author=Arita K, Hashimoto H, Shimizu T, ''et al.'' |title=Structural basis for Ca(2+)-induced activation of human PAD4. |journal=Nat. Struct. Mol. Biol. |volume=11 |issue= 8 |pages= 777-83 |year= 2004 |pmid= 15247907 |doi= 10.1038/nsmb799 }}
*{{cite journal   |vauthors=Arita K, Hashimoto H, Shimizu T, etal |title=Structural basis for Ca(2+)-induced activation of human PAD4. |journal=Nat. Struct. Mol. Biol. |volume=11 |issue= 8 |pages= 777–83 |year= 2004 |pmid= 15247907 |doi= 10.1038/nsmb799 }}
*{{cite journal | author=Hoppe B, Heymann GA, Tolou F, ''et al.'' |title=High variability of peptidylarginine deiminase 4 (PADI4) in a healthy white population: characterization of six new variants of PADI4 exons 2-4 by a novel haplotype-specific sequencing-based approach. |journal=J. Mol. Med. |volume=82 |issue= 11 |pages= 762-7 |year= 2005 |pmid= 15338034 |doi= 10.1007/s00109-004-0584-6 }}
*{{cite journal   |vauthors=Hoppe B, Heymann GA, Tolou F, etal |title=High variability of peptidylarginine deiminase 4 (PADI4) in a healthy white population: characterization of six new variants of PADI4 exons 2-4 by a novel haplotype-specific sequencing-based approach. |journal=J. Mol. Med. |volume=82 |issue= 11 |pages= 762–7 |year= 2005 |pmid= 15338034 |doi= 10.1007/s00109-004-0584-6 }}
*{{cite journal | author=Cuthbert GL, Daujat S, Snowden AW, ''et al.'' |title=Histone deimination antagonizes arginine methylation. |journal=Cell |volume=118 |issue= 5 |pages= 545-53 |year= 2004 |pmid= 15339660 |doi= 10.1016/j.cell.2004.08.020 }}
*{{cite journal   |vauthors=Cuthbert GL, Daujat S, Snowden AW, etal |title=Histone deimination antagonizes arginine methylation. |journal=Cell |volume=118 |issue= 5 |pages= 545–53 |year= 2004 |pmid= 15339660 |doi= 10.1016/j.cell.2004.08.020 }}
*{{cite journal | author=Wang Y, Wysocka J, Sayegh J, ''et al.'' |title=Human PAD4 regulates histone arginine methylation levels via demethylimination. |journal=Science |volume=306 |issue= 5694 |pages= 279-83 |year= 2004 |pmid= 15345777 |doi= 10.1126/science.1101400 }}
*{{cite journal   |vauthors=Wang Y, Wysocka J, Sayegh J, etal |title=Human PAD4 regulates histone arginine methylation levels via demethylimination. |journal=Science |volume=306 |issue= 5694 |pages= 279–83 |year= 2004 |pmid= 15345777 |doi= 10.1126/science.1101400 }}
*{{cite journal | author=Gerhard DS, Wagner L, Feingold EA, ''et al.'' |title=The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). |journal=Genome Res. |volume=14 |issue= 10B |pages= 2121-7 |year= 2004 |pmid= 15489334 |doi= 10.1101/gr.2596504 }}
*{{cite journal   |vauthors=Gerhard DS, Wagner L, Feingold EA, etal |title=The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). |journal=Genome Res. |volume=14 |issue= 10B |pages= 2121–7 |year= 2004 |pmid= 15489334 |doi= 10.1101/gr.2596504 | pmc=528928 }}
*{{cite journal | author=Nakayama-Hamada M, Suzuki A, Kubota K, ''et al.'' |title=Comparison of enzymatic properties between hPADI2 and hPADI4. |journal=Biochem. Biophys. Res. Commun. |volume=327 |issue= 1 |pages= 192-200 |year= 2005 |pmid= 15629448 |doi= 10.1016/j.bbrc.2004.11.152 }}
*{{cite journal   |vauthors=Nakayama-Hamada M, Suzuki A, Kubota K, etal |title=Comparison of enzymatic properties between hPADI2 and hPADI4. |journal=Biochem. Biophys. Res. Commun. |volume=327 |issue= 1 |pages= 192–200 |year= 2005 |pmid= 15629448 |doi= 10.1016/j.bbrc.2004.11.152 }}
*{{cite journal | author=Lee YH, Coonrod SA, Kraus WL, ''et al.'' |title=Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=102 |issue= 10 |pages= 3611-6 |year= 2005 |pmid= 15731352 |doi= 10.1073/pnas.0407159102 }}
*{{cite journal   |vauthors=Lee YH, Coonrod SA, Kraus WL, etal |title=Regulation of coactivator complex assembly and function by protein arginine methylation and demethylimination. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=102 |issue= 10 |pages= 3611–6 |year= 2005 |pmid= 15731352 |doi= 10.1073/pnas.0407159102 | pmc=553305 }}
*{{cite journal | author=Kearney PL, Bhatia M, Jones NG, ''et al.'' |title=Kinetic characterization of protein arginine deiminase 4: a transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis. |journal=Biochemistry |volume=44 |issue= 31 |pages= 10570-82 |year= 2005 |pmid= 16060666 |doi= 10.1021/bi050292m }}
*{{cite journal   |vauthors=Kearney PL, Bhatia M, Jones NG, etal |title=Kinetic characterization of protein arginine deiminase 4: a transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis. |journal=Biochemistry |volume=44 |issue= 31 |pages= 10570–82 |year= 2005 |pmid= 16060666 |doi= 10.1021/bi050292m }}
*{{cite journal | author=Ikari K, Kuwahara M, Nakamura T, ''et al.'' |title=Association between PADI4 and rheumatoid arthritis: a replication study. |journal=Arthritis Rheum. |volume=52 |issue= 10 |pages= 3054-7 |year= 2005 |pmid= 16200584 |doi= 10.1002/art.21309 }}
*{{cite journal   |vauthors=Ikari K, Kuwahara M, Nakamura T, etal |title=Association between PADI4 and rheumatoid arthritis: a replication study. |journal=Arthritis Rheum. |volume=52 |issue= 10 |pages= 3054–7 |year= 2005 |pmid= 16200584 |doi= 10.1002/art.21309 }}
*{{cite journal  | author=Chang X, Han J |title=Expression of peptidylarginine deiminase type 4 (PAD4) in various tumors. |journal=Mol. Carcinog. |volume=45 |issue= 3 |pages= 183-96 |year= 2006 |pmid= 16355400 |doi= 10.1002/mc.20169 }}
*{{cite journal  | vauthors=Chang X, Han J |title=Expression of peptidylarginine deiminase type 4 (PAD4) in various tumors. |journal=Mol. Carcinog. |volume=45 |issue= 3 |pages= 183–96 |year= 2006 |pmid= 16355400 |doi= 10.1002/mc.20169 }}
*{{cite journal | author=Plenge RM, Padyukov L, Remmers EF, ''et al.'' |title=Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. |journal=Am. J. Hum. Genet. |volume=77 |issue= 6 |pages= 1044-60 |year= 2006 |pmid= 16380915 |doi= 10.1086/498651 }}
*{{cite journal   |vauthors=Plenge RM, Padyukov L, Remmers EF, etal |title=Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. |journal=Am. J. Hum. Genet. |volume=77 |issue= 6 |pages= 1044–60 |year= 2006 |pmid= 16380915 |doi= 10.1086/498651 | pmc=1285162 }}
*{{cite journal | author=Hoppe B, Häupl T, Gruber R, ''et al.'' |title=Detailed analysis of the variability of peptidylarginine deiminase type 4 in German patients with rheumatoid arthritis: a case-control study. |journal=Arthritis Res. Ther. |volume=8 |issue= 2 |pages= R34 |year= 2006 |pmid= 16469113 |doi= 10.1186/ar1889 }}
*{{cite journal   |vauthors=Hoppe B, Häupl T, Gruber R, etal |title=Detailed analysis of the variability of peptidylarginine deiminase type 4 in German patients with rheumatoid arthritis: a case-control study. |journal=[[Arthritis Research & Therapy]] |volume=8 |issue= 2 |pages= R34 |year= 2006 |pmid= 16469113 |doi= 10.1186/ar1889 | pmc=1526594 }}
}}
}}
{{refend}}
{{refend}}
{{PDB Gallery|geneid=23569}}


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Latest revision as of 17:29, 7 September 2017

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Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez

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Ensembl

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UniProt

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RefSeq (mRNA)

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RefSeq (protein)

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Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human

Peptidyl arginine deiminase, type IV, also known as PADI4, is a human protein which in humans is encoded by the PADI4 gene.[1][2]

Molecular biology

The human gene is found on the short arm of Chromosome 1 near the telomere (1p36.13). It is located on the Watson (plus) strand and is 55,806 bases long. The protein is 663 amino acids long with a molecular weight of 74,095 Da.[1]

Function

This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response.[2] PADI4 plays a role in the epigenetics, the deimination of arginines on histones 3 and 4 can act antagonistically to arginine methylation (Chromatin modifications and their function, Kouzarides 2007, Cell, review)

The protein may be found in oligomers and binds 5 calcium ions per subunit. It catalyses the reaction:

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

Subcellular and tissue distribution

It is normally found in the cytoplasm, nucleus and in cytoplasmic granules of eosinophils and neutrophils. It is not expressed in peripheral monocytes or lymphocytes. It is also expressed in rheumatoid arthritis synovial tissues.

References

  1. ↑ 1.0 1.1 Nakashima K, Hagiwara T, Ishigami A, Nagata S, Asaga H, Kuramoto M, Senshu T, Yamada M (September 1999). "Molecular characterization of peptidylarginine deiminase in HL-60 cells induced by retinoic acid and 1alpha,25-dihydroxyvitamin D(3)". J. Biol. Chem. 274 (39): 27786–92. doi:10.1074/jbc.274.39.27786. PMID 10488123.
  2. ↑ 2.0 2.1 "Entrez Gene: PADI4 peptidyl arginine deiminase, type IV".

Further reading


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