This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

7dan

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Structure of the Ca2+-bound wild-type peptidylarginine deiminase type III (PAD3)

Structural highlights

7dan is a 3 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 3.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PADI3_HUMAN Uncombable hair syndrome. The disease is caused by mutations affecting the gene represented in this entry.

Function

PADI3_HUMAN Catalyzes the deimination of arginine residues of proteins.^[1]

Publication Abstract from PubMed

Peptidylarginine deiminase type III (PAD3) is an isozyme belonging to the PAD enzyme family that converts arginine to citrulline residue(s) within proteins. PAD3 is expressed in most differentiated keratinocytes of the epidermis and hair follicles, while S100A3, trichohyalin, and filaggrin are its principal substrates. In this study, the X-ray crystal structures of PAD3 in six states, including its complex with the PAD inhibitor Cl-amidine, were determined. This structural analysis identified a large space around Gly374 in the PAD3-Ca(2+)-Cl-amidine complex, which may be used to develop novel PAD3-selective inhibitors. In addition, similarities between PAD3 and PAD4 were found based on the investigation of PAD4 reactivity with S100A3 in vitro. A comparison of the structures of PAD1, PAD2, PAD3, and PAD4 implied that the flexibility of the structures around the active site may lead to different substrate selectivity among these PAD isozymes.

Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design.,Funabashi K, Sawata M, Nagai A, Akimoto M, Mashimo R, Takahara H, Kizawa K, Thompson PR, Ite K, Kitanishi K, Unno M Arch Biochem Biophys. 2021 May 7:108911. doi: 10.1016/j.abb.2021.108911. PMID:33971157^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ U Basmanav FB, Cau L, Tafazzoli A, Mechin MC, Wolf S, Romano MT, Valentin F, Wiegmann H, Huchenq A, Kandil R, Garcia Bartels N, Kilic A, George S, Ralser DJ, Bergner S, Ferguson DJP, Oprisoreanu AM, Wehner M, Thiele H, Altmuller J, Nurnberg P, Swan D, Houniet D, Buchner A, Weibel L, Wagner N, Grimalt R, Bygum A, Serre G, Blume-Peytavi U, Sprecher E, Schoch S, Oji V, Hamm H, Farrant P, Simon M, Betz RC. Mutations in Three Genes Encoding Proteins Involved in Hair Shaft Formation Cause Uncombable Hair Syndrome. Am J Hum Genet. 2016 Dec 1;99(6):1292-1304. doi: 10.1016/j.ajhg.2016.10.004. Epub, 2016 Nov 17. PMID:27866708 doi:http://dx.doi.org/10.1016/j.ajhg.2016.10.004
↑ Funabashi K, Sawata M, Nagai A, Akimoto M, Mashimo R, Takahara H, Kizawa K, Thompson PR, Ite K, Kitanishi K, Unno M. Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design. Arch Biochem Biophys. 2021 May 7:108911. doi: 10.1016/j.abb.2021.108911. PMID:33971157 doi:http://dx.doi.org/10.1016/j.abb.2021.108911

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7dan"

Categories: Homo sapiens | Large Structures | Sawata M | Unno M

@@ Line 3: / Line 3: @@
 <StructureSection load='7dan' size='340' side='right'caption='[[7dan]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7dan]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7DAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DAN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7dan]] is a 3 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=7DAN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7DAN FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7d8n|7d8n]], [[7d5r|7d5r]], [[7d5v|7d5v]], [[7d56|7d56]], [[7d4y|7d4y]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PADI3, PAD3, PDI3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Protein-arginine_deiminase Protein-arginine deiminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.15 3.5.3.15] </span></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7dan FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7dan OCA], [https://pdbe.org/7dan PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7dan RCSB], [https://www.ebi.ac.uk/pdbsum/7dan PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7dan ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[https://www.uniprot.org/uniprot/PADI3_HUMAN PADI3_HUMAN]] Uncombable hair syndrome. The disease is caused by mutations affecting the gene represented in this entry.
+[https://www.uniprot.org/uniprot/PADI3_HUMAN PADI3_HUMAN] Uncombable hair syndrome. The disease is caused by mutations affecting the gene represented in this entry.
 == Function ==
-[[https://www.uniprot.org/uniprot/PADI3_HUMAN PADI3_HUMAN]] Catalyzes the deimination of arginine residues of proteins.<ref>PMID:27866708</ref>
+[https://www.uniprot.org/uniprot/PADI3_HUMAN PADI3_HUMAN] Catalyzes the deimination of arginine residues of proteins.<ref>PMID:27866708</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 25: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Protein-arginine deiminase]]
+[[Category: Sawata M]]
-[[Category: Sawata, M]]
+[[Category: Unno M]]
-[[Category: Unno, M]]
-[[Category: Active form]]
-[[Category: Calcium]]
-[[Category: Citrullination]]
-[[Category: Enzyme]]
-[[Category: Hydrolase]]
-[[Category: Isozyme]]
-[[Category: Peptidylarginie deiminase]]
-[[Category: Post-translational modification]]

7dan

From Proteopedia

Current revision

Structure of the Ca2+-bound wild-type peptidylarginine deiminase type III (PAD3)

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox