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PDBsum entry 1wd8

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protein links
Hydrolase PDB id
1wd8
Jmol
Contents
Protein chain
559 a.a. *
* Residue conservation analysis
PDB id:
1wd8
Name: Hydrolase
Title: Calcium free form of human peptidylarginine deiminase type4
Structure: Protein-arginine deiminase type iv. Chain: a. Synonym: peptidylarginine deiminase iv, hl-60 pad. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.80Å     R-factor:   0.234     R-free:   0.264
Authors: K.Arita,H.Hashimoto,T.Shimizu,K.Nakashima,M.Yamada,M.Sato
Key ref:
K.Arita et al. (2004). Structural basis for Ca(2+)-induced activation of human PAD4. Nat Struct Mol Biol, 11, 777-783. PubMed id: 15247907 DOI: 10.1038/nsmb799
Date:
12-May-04     Release date:   13-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UM07  (PADI4_HUMAN) -  Protein-arginine deiminase type-4
Seq:
Struc:
 
Seq:
Struc:
663 a.a.
559 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.5.3.15  - Protein-arginine deiminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein L-arginine + H2O = protein L-citrulline + NH3
Protein L-arginine
+ H(2)O
= protein L-citrulline
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     immune system process   12 terms 
  Biochemical function     protein binding     6 terms  

 

 
    Added reference    
 
 
DOI no: 10.1038/nsmb799 Nat Struct Mol Biol 11:777-783 (2004)
PubMed id: 15247907  
 
 
Structural basis for Ca(2+)-induced activation of human PAD4.
K.Arita, H.Hashimoto, T.Shimizu, K.Nakashima, M.Yamada, M.Sato.
 
  ABSTRACT  
 
Peptidylarginine deiminase 4 (PAD4) is a Ca(2+)-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. Its gene is a susceptibility locus for rheumatoid arthritis. Here we present the crystal structure of Ca(2+)-free wild-type PAD4, which shows that the polypeptide chain adopts an elongated fold in which the N-terminal domain forms two immunoglobulin-like subdomains, and the C-terminal domain forms an alpha/beta propeller structure. Five Ca(2+)-binding sites, none of which adopt an EF-hand motif, were identified in the structure of a Ca(2+)-bound inactive mutant with and without bound substrate. These structural data indicate that Ca(2+) binding induces conformational changes that generate the active site cleft. Our findings identify a novel mechanism for enzyme activation by Ca(2+) ions, and are important for understanding the mechanism of protein citrullination and for developing PAD-inhibiting drugs for the treatment of rheumatoid arthritis.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Structure of the substrate- and Ca^2+-binding sites in PAD4. The |F[o]| - |F[c]| electron densities, contoured at 8 and in orange, that correspond to Ca^2+ ions are superimposed. Ca^2+ ions are black balls. (a) Left, structure surrounding Ca1, Ca2 and the substrate, benzoyl-L-arginine amide, in the C-terminal domain. The substrate is a green stick model. Superimposed is |F[o]| - |F[c]| electron density of the substrate, contoured at 2 . Right, schematic diagram of the structure on the left (bond lengths in red in ). (b) Left, structure surrounding Ca3, Ca4 and Ca5 in the N-terminal domain. Right, schematic diagram of the structure on the left, with bond lengths as in a.
Figure 5.
Figure 5. Proposed reaction mechanism of protein citrullination by PAD4.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 777-783) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377473 M.Unno, T.Kawasaki, H.Takahara, C.W.Heizmann, and K.Kizawa (2011).
Refined crystal structures of human Ca(2+)/Zn(2+)-binding S100A3 protein characterized by two disulfide bridges.
  J Mol Biol, 408, 477-490.
PDB codes: 3nsi 3nsk 3nsl 3nso
19693695 A.Rebl, B.Köllner, E.Anders, K.Wimmers, and T.Goldammer (2010).
Peptidylarginine deiminase gene is differentially expressed in freshwater and brackish water rainbow trout.
  Mol Biol Rep, 37, 2333-2339.  
20013286 B.Jang, J.K.Jin, Y.C.Jeon, H.J.Cho, A.Ishigami, K.C.Choi, R.I.Carp, N.Maruyama, Y.S.Kim, and E.K.Choi (2010).
Involvement of peptidylarginine deiminase-mediated post-translational citrullination in pathogenesis of sporadic Creutzfeldt-Jakob disease.
  Acta Neuropathol, 119, 199-210.  
20014086 B.Knuckley, C.P.Causey, P.J.Pellechia, P.F.Cook, and P.R.Thompson (2010).
Haloacetamidine-based inactivators of protein arginine deiminase 4 (PAD4): evidence that general acid catalysis promotes efficient inactivation.
  Chembiochem, 11, 161-165.  
20201080 F.Andrade, E.Darrah, M.Gucek, R.N.Cole, A.Rosen, and X.Zhu (2010).
Autocitrullination of human peptidyl arginine deiminase type 4 regulates protein citrullination during cell activation.
  Arthritis Rheum, 62, 1630-1640.  
20192990 H.Uysal, K.S.Nandakumar, C.Kessel, S.Haag, S.Carlsen, H.Burkhardt, and R.Holmdahl (2010).
Antibodies to citrullinated proteins: molecular interactions and arthritogenicity.
  Immunol Rev, 233, 9.  
20036411 J.E.Jones, C.P.Causey, L.Lovelace, B.Knuckley, H.Flick, L.Lebioda, and P.R.Thompson (2010).
Characterization and inactivation of an agmatine deiminase from Helicobacter pylori.
  Bioorg Chem, 38, 62-73.
PDB code: 3hvm
20111885 M.C.Méchin, F.Coudane, V.Adoue, J.Arnaud, H.Duplan, M.Charveron, A.M.Schmitt, H.Takahara, G.Serre, and M.Simon (2010).
Deimination is regulated at multiple levels including auto-deimination of peptidylarginine deiminases.
  Cell Mol Life Sci, 67, 1491-1503.  
20190809 P.Li, D.Wang, H.Yao, P.Doret, G.Hao, Q.Shen, H.Qiu, X.Zhang, Y.Wang, G.Chen, and Y.Wang (2010).
Coordination of PAD4 and HDAC2 in the regulation of p53-target gene expression.
  Oncogene, 29, 3153-3162.  
20553633 P.Mangat, N.Wegner, P.J.Venables, and J.Potempa (2010).
Bacterial and human peptidylarginine deiminases: targets for inhibiting the autoimmune response in rheumatoid arthritis?
  Arthritis Res Ther, 12, 209.  
20222985 X.Chang, and K.Fang (2010).
PADI4 and tumourigenesis.
  Cancer Cell Int, 10, 7.  
18603028 B.C.Smith, and J.M.Denu (2009).
Chemical mechanisms of histone lysine and arginine modifications.
  Biochim Biophys Acta, 1789, 45-57.  
19581286 H.Denis, R.Deplus, P.Putmans, M.Yamada, R.Métivier, and F.Fuks (2009).
Functional connection between deimination and deacetylation of histones.
  Mol Cell Biol, 29, 4982-4993.  
19040354 M.E.Stensland, S.Pollmann, ..Molberg, L.M.Sollid, and B.Fleckenstein (2009).
Primary sequence, together with other factors, influence peptide deimination by peptidylarginine deiminase-4.
  Biol Chem, 390, 99.  
19545534 S.B.Rodríguez, B.L.Stitt, and D.E.Ash (2009).
Expression of peptidylarginine deiminase from Porphyromonas gingivalis in Escherichia coli: enzyme purification and characterization.
  Arch Biochem Biophys, 488, 14-22.  
20028143 Z.Ke, S.Wang, D.Xie, and Y.Zhang (2009).
Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.
  J Phys Chem B, 113, 16705-16710.  
19507815 Z.Ke, Y.Zhou, P.Hu, S.Wang, D.Xie, and Y.Zhang (2009).
Active site cysteine is protonated in the PAD4 Michaelis complex: evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations.
  J Phys Chem B, 113, 12750-12758.  
18923545 A.A.Musse, E.Polverini, R.Raijmakers, and G.Harauz (2008).
Kinetics of human peptidylarginine deiminase 2 (hPAD2)--reduction of Ca2+ dependence by phospholipids and assessment of proposed inhibition by paclitaxel side chains.
  Biochem Cell Biol, 86, 437-447.  
18463355 A.J.Snow, P.Puri, A.Acker-Palmer, T.Bouwmeester, S.Vijayaraghavan, and D.Kline (2008).
Phosphorylation-dependent interaction of tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein (YWHA) with PADI6 following oocyte maturation in mice.
  Biol Reprod, 79, 337-347.  
19086853 K.Tilleman, and D.Deforce (2008).
Proteomics in rheumatology.
  Expert Rev Proteomics, 5, 755-759.  
18576335 M.L.Harris, E.Darrah, G.K.Lam, S.J.Bartlett, J.T.Giles, A.V.Grant, P.Gao, W.W.Scott, H.El-Gabalawy, L.Casciola-Rosen, K.C.Barnes, J.M.Bathon, and A.Rosen (2008).
Association of autoimmunity to peptidyl arginine deiminase type 4 with genotype and disease severity in rheumatoid arthritis.
  Arthritis Rheum, 58, 1958-1967.  
18505818 P.Li, H.Yao, Z.Zhang, M.Li, Y.Luo, P.R.Thompson, D.S.Gilmour, and Y.Wang (2008).
Regulation of p53 target gene expression by peptidylarginine deiminase 4.
  Mol Cell Biol, 28, 4745-4758.  
18482699 T.W.Linsky, A.F.Monzingo, E.M.Stone, J.D.Robertus, and W.Fast (2008).
Promiscuous partitioning of a covalent intermediate common in the pentein superfamily.
  Chem Biol, 15, 467-475.
PDB code: 3bpb
17893996 A.Suzuki, R.Yamada, and K.Yamamoto (2007).
Citrullination by peptidylarginine deiminase in rheumatoid arthritis.
  Ann N Y Acad Sci, 1108, 323-339.  
17497940 B.Knuckley, M.Bhatia, and P.R.Thompson (2007).
Protein arginine deiminase 4: evidence for a reverse protonation mechanism.
  Biochemistry, 46, 6578-6587.  
17468392 F.Bachand (2007).
Protein arginine methyltransferases: from unicellular eukaryotes to humans.
  Eukaryot Cell, 6, 889-898.  
16900293 G.Harauz, and A.A.Musse (2007).
A tale of two citrullines--structural and functional aspects of myelin basic protein deimination in health and disease.
  Neurochem Res, 32, 137-158.  
17216583 H.C.Hung, C.Y.Lin, Y.F.Liao, P.C.Hsu, G.J.Tsay, and G.Y.Liu (2007).
The functional haplotype of peptidylarginine deiminase IV (S55G, A82V and A112G) associated with susceptibility to rheumatoid arthritis dominates apoptosis of acute T leukemia Jurkat cells.
  Apoptosis, 12, 475-487.  
20477107 J.Risteli, M.K.Koivula, and L.Risteli (2007).
Citrullinated collagens in the pathogenesis of rheumatoid arthritis.
  Expert Rev Clin Immunol, 3, 187-194.  
18489346 M.C.Méchin, M.Sebbag, J.Arnaud, R.Nachat, C.Foulquier, V.Adoue, F.Coudane, H.Duplan, A.M.Schmitt, S.Chavanas, M.Guerrin, G.Serre, and M.Simon (2007).
Update on peptidylarginine deiminases and deimination in skin physiology and severe human diseases.
  Int J Cosmet Sci, 29, 147-168.  
17600152 O.Braun, M.Knipp, S.Chesnov, and M.Vasák (2007).
Specific reactions of S-nitrosothiols with cysteine hydrolases: A comparative study between dimethylargininase-1 and CTP synthetase.
  Protein Sci, 16, 1522-1534.  
17469103 S.Cha, C.B.Choi, T.U.Han, C.P.Kang, C.Kang, and S.C.Bae (2007).
Association of anti-cyclic citrullinated peptide antibody levels with PADI4 haplotypes in early rheumatoid arthritis and with shared epitope alleles in very late rheumatoid arthritis.
  Arthritis Rheum, 56, 1454-1463.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
17603254 Y.Naishiro, C.Suzuki, M.Kimura, M.Yamamoto, H.Takahashi, H.Sohma, T.Hori, Y.Shinomura, Y.Kokai, and K.Imai (2007).
[Plasma analysis of rheumatoid arthritis by SELDI]
  Nihon Rinsho Meneki Gakkai Kaishi, 30, 145-150.  
17080455 Y.Wei, H.Zhou, Y.Sun, Y.He, and Y.Luo (2007).
Insight into the catalytic mechanism of arginine deiminase: functional studies on the crucial sites.
  Proteins, 66, 740-750.  
16730216 B.György, E.Tóth, E.Tarcsa, A.Falus, and E.I.Buzás (2006).
Citrullination: a posttranslational modification in health and disease.
  Int J Biochem Cell Biol, 38, 1662-1677.  
16469113 B.Hoppe, T.Häupl, R.Gruber, H.Kiesewetter, G.R.Burmester, A.Salama, and T.Dörner (2006).
Detailed analysis of the variability of peptidylarginine deiminase type 4 in German patients with rheumatoid arthritis: a case-control study.
  Arthritis Res Ther, 8, R34.  
16698551 D.Frey, O.Braun, C.Briand, M.Vasák, and M.G.Grütter (2006).
Structure of the mammalian NOS regulator dimethylarginine dimethylaminohydrolase: A basis for the design of specific inhibitors.
  Structure, 14, 901-911.
PDB codes: 2c6z 2ci1 2ci3 2ci4 2ci5 2ci6 2ci7
16502257 G.Y.Liu, Y.F.Liao, W.H.Chang, C.C.Liu, M.C.Hsieh, P.C.Hsu, G.J.Tsay, and H.C.Hung (2006).
Overexpression of peptidylarginine deiminase IV features in apoptosis of haematopoietic cells.
  Apoptosis, 11, 183-196.  
16779844 H.Shirai, Y.Mokrab, and K.Mizuguchi (2006).
The guanidino-group modifying enzymes: structural basis for their diversity and commonality.
  Proteins, 64, 1010-1023.  
16567635 K.Arita, T.Shimizu, H.Hashimoto, Y.Hidaka, M.Yamada, and M.Sato (2006).
Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4.
  Proc Natl Acad Sci U S A, 103, 5291-5296.
PDB codes: 2dew 2dex 2dey
17090024 Y.Luo, B.Knuckley, M.Bhatia, P.J.Pellechia, and P.R.Thompson (2006).
Activity-based protein profiling reagents for protein arginine deiminase 4 (PAD4): synthesis and in vitro evaluation of a fluorescently labeled probe.
  J Am Chem Soc, 128, 14468-14469.  
16433522 Y.Luo, B.Knuckley, Y.H.Lee, M.R.Stallcup, and P.R.Thompson (2006).
A fluoroacetamidine-based inactivator of protein arginine deiminase 4: design, synthesis, and in vitro and in vivo evaluation.
  J Am Chem Soc, 128, 1092-1093.  
17002273 Y.Luo, K.Arita, M.Bhatia, B.Knuckley, Y.H.Lee, M.R.Stallcup, M.Sato, and P.R.Thompson (2006).
Inhibitors and inactivators of protein arginine deiminase 4: functional and structural characterization.
  Biochemistry, 45, 11727-11736.
PDB code: 2dw5
16091358 A.Galkin, X.Lu, D.Dunaway-Mariano, and O.Herzberg (2005).
Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase.
  J Biol Chem, 280, 34080-34087.
PDB codes: 2a9g 2aaf 2abr 2aci
15700232 K.Kubota, T.Yoneyama-Takazawa, and K.Ichikawa (2005).
Determination of sites citrullinated by peptidylarginine deiminase using 18O stable isotope labeling and mass spectrometry.
  Rapid Commun Mass Spectrom, 19, 683-688.  
16271291 K.Yamamoto, and R.Yamada (2005).
Genome-wide single nucleotide polymorphism analyses of rheumatoid arthritis.
  J Autoimmun, 25, 12-15.  
15982300 R.Nachat, M.C.Méchin, M.Charveron, G.Serre, J.Constans, and M.Simon (2005).
Peptidylarginine deiminase isoforms are differentially expressed in the anagen hair follicles and other human skin appendages.
  J Invest Dermatol, 125, 34-41.  
15345777 Y.Wang, J.Wysocka, J.Sayegh, Y.H.Lee, J.R.Perlin, L.Leonelli, L.S.Sonbuchner, C.H.McDonald, R.G.Cook, Y.Dou, R.G.Roeder, S.Clarke, M.R.Stallcup, C.D.Allis, and S.A.Coonrod (2004).
Human PAD4 regulates histone arginine methylation levels via demethylimination.
  Science, 306, 279-283.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.