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[[Image:4dkt.jpg|left|200px]]


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==Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide==
The line below this paragraph, containing "STRUCTURE_4dkt", creates the "Structure Box" on the page.
<StructureSection load='4dkt' size='340' side='right'caption='[[4dkt]], [[Resolution|resolution]] 2.98&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[4dkt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DKT FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.98&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FIO:N~5~-[(1E)-2-FLUOROETHANIMIDOYL]-L-ORNITHINE'>FIO</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_4dkt|  PDB=4dkt  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dkt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dkt OCA], [https://pdbe.org/4dkt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dkt RCSB], [https://www.ebi.ac.uk/pdbsum/4dkt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dkt ProSAT]</span></td></tr>
 
</table>
===Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide===
== Disease ==
 
[https://www.uniprot.org/uniprot/PADI4_HUMAN PADI4_HUMAN] Genetic variations in PADI4 are a cause of susceptibility to rheumatoid arthritis (RA) [MIM:[https://omim.org/entry/180300 180300]. It is a systemic inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. Note=Could have an important role in the pathogenesis of rheumatoid arthritis by increasing citrullination of proteins in rheumatoid arthritis synovial tissues, leading, in a cytokine-rich milieu, to a break in tolerance to citrullinated peptides processed and presented in the appropriate HLA context.<ref>PMID:12833157</ref>
 
== Function ==
<!--
[https://www.uniprot.org/uniprot/PADI4_HUMAN PADI4_HUMAN] Catalyzes the citrullination/deimination of arginine residues of proteins. Citrullinates histone H3 at 'Arg-8' and/or 'Arg-17' and histone H4 at 'Arg-3', which prevents their methylation by CARM1 and HRMT1L2/PRMT1 and represses transcription. Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1.<ref>PMID:15339660</ref> <ref>PMID:15345777</ref>
The line below this paragraph, {{ABSTRACT_PUBMED_22004374}}, adds the Publication Abstract to the page
== References ==
(as it appears on PubMed at http://www.pubmed.gov), where 22004374 is the PubMed ID number.
<references/>
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__TOC__
{{ABSTRACT_PUBMED_22004374}}
</StructureSection>
 
==About this Structure==
[[4dkt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DKT OCA].  
 
==Reference==
<ref group="xtra">PMID:022004374</ref><references group="xtra"/>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Protein-arginine deiminase]]
[[Category: Large Structures]]
[[Category: Causey, C P.]]
[[Category: Causey CP]]
[[Category: Coonrod, S A.]]
[[Category: Coonrod SA]]
[[Category: Fang, P.]]
[[Category: Fang P]]
[[Category: Guo, M.]]
[[Category: Guo M]]
[[Category: Jones, J E.]]
[[Category: Jones JE]]
[[Category: Slack, J L.]]
[[Category: Slack JL]]
[[Category: Subramanian, V.]]
[[Category: Subramanian V]]
[[Category: Thompson, P R.]]
[[Category: Thompson PR]]
[[Category: Zhang, X.]]
[[Category: Zhang X]]
[[Category: Alpha/beta-propeller]]
[[Category: Arginine citrullination]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Immunoglobulin-like]]
[[Category: Post-translational]]

Latest revision as of 17:37, 14 March 2024

Crystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamideCrystal structure of human peptidylarginine deiminase 4 in complex with N-acetyl-L-threonyl-L-alpha-aspartyl-N5-[(1E)-2-fluoroethanimidoyl]-L-ornithinamide

Structural highlights

4dkt is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.98Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PADI4_HUMAN Genetic variations in PADI4 are a cause of susceptibility to rheumatoid arthritis (RA) [MIM:180300. It is a systemic inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. Note=Could have an important role in the pathogenesis of rheumatoid arthritis by increasing citrullination of proteins in rheumatoid arthritis synovial tissues, leading, in a cytokine-rich milieu, to a break in tolerance to citrullinated peptides processed and presented in the appropriate HLA context.[1]

Function

PADI4_HUMAN Catalyzes the citrullination/deimination of arginine residues of proteins. Citrullinates histone H3 at 'Arg-8' and/or 'Arg-17' and histone H4 at 'Arg-3', which prevents their methylation by CARM1 and HRMT1L2/PRMT1 and represses transcription. Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1.[2] [3]

References

  1. ↑ Suzuki A, Yamada R, Chang X, Tokuhiro S, Sawada T, Suzuki M, Nagasaki M, Nakayama-Hamada M, Kawaida R, Ono M, Ohtsuki M, Furukawa H, Yoshino S, Yukioka M, Tohma S, Matsubara T, Wakitani S, Teshima R, Nishioka Y, Sekine A, Iida A, Takahashi A, Tsunoda T, Nakamura Y, Yamamoto K. Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat Genet. 2003 Aug;34(4):395-402. PMID:12833157 doi:10.1038/ng1206
  2. ↑ Cuthbert GL, Daujat S, Snowden AW, Erdjument-Bromage H, Hagiwara T, Yamada M, Schneider R, Gregory PD, Tempst P, Bannister AJ, Kouzarides T. Histone deimination antagonizes arginine methylation. Cell. 2004 Sep 3;118(5):545-53. PMID:15339660 doi:10.1016/j.cell.2004.08.020
  3. ↑ Wang Y, Wysocka J, Sayegh J, Lee YH, Perlin JR, Leonelli L, Sonbuchner LS, McDonald CH, Cook RG, Dou Y, Roeder RG, Clarke S, Stallcup MR, Allis CD, Coonrod SA. Human PAD4 regulates histone arginine methylation levels via demethylimination. Science. 2004 Oct 8;306(5694):279-83. Epub 2004 Sep 2. PMID:15345777 doi:10.1126/science.1101400

4dkt, resolution 2.98Å

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