3APN

Crystal structure of the human wild-type PAD4 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene

Horikoshi, N.Tachiwana, H.Saito, K.Osakabe, A.Sato, M.Yamada, M.Akashi, S.Nishimura, Y.Kagawa, W.Kurumizaka, H.

(2011) Acta Crystallogr.,Sect.D 67: 112-118

  • DOI: 10.1107/S0907444910051711
  • Primary Citation of Related Structures:  3APM

  • PubMed Abstract: 
  • PAD4 is a peptidylarginine deiminase that catalyzes citrullination, a type of post-translational modification. In this reaction, arginine residues in proteins are converted to citrulline. PAD4 promotes the deimination of arginine residues in histones ...

    PAD4 is a peptidylarginine deiminase that catalyzes citrullination, a type of post-translational modification. In this reaction, arginine residues in proteins are converted to citrulline. PAD4 promotes the deimination of arginine residues in histones and may regulate transcription in the context of the chromatin. Single-nucleotide polymorphisms (SNP) in the gene encoding PAD4 identified it as one of the genes associated with susceptibility to rheumatoid arthritis. The PAD4 SNP involve three amino-acid substitutions: Ser55 to Gly, Ala82 to Val and Ala112 to Gly. Autoantibodies for improperly citrullinated proteins have been found in rheumatoid arthritis patients, suggesting that the PAD4(SNP) mRNA is more stable than the conventional PAD4 mRNA and/or the PAD4(SNP) protein possesses a higher citrullination activity than the PAD4 protein. In order to study the effects of the three amino-acid substitutions found in PAD4(SNP), the crystal structure of PAD4(SNP) was determined and it was found that the amino-acid substitutions in PAD4(SNP) only induced conformational changes within the N-terminal domain, not in the active centre for citrullination located in the C-terminal domain. Biochemical analyses also suggested that the citrullination activity of PAD4(SNP) may not substantially differ from that of conventional PAD4. These structural and biochemical findings suggested that the improper protein citrullination found in rheumatoid arthritis patients is not caused by defects in the citrullination activity of PAD4(SNP) but by other reasons such as enhanced PAD4(SNP) mRNA stability.


    Organizational Affiliation

    Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjyuku-ku, Tokyo 162-8480, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-arginine deiminase type-4
A
666Homo sapiensGene Names: PADI4 (PAD4, PADI5, PDI5)
EC: 3.5.3.15
Find proteins for Q9UM07 (Homo sapiens)
Go to Gene View: PADI4
Go to UniProtKB:  Q9UM07
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.254α = 90.00
b = 61.064β = 123.74
c = 113.569γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
BSSdata collection
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-04-11
    Type: Database references