1WD8

Calcium free form of human peptidylarginine deiminase type4 (PAD4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for Ca(2+)-induced activation of human PAD4

Arita, K.Hashimoto, H.Shimizu, T.Nakashima, K.Yamada, M.Sato, M.

(2004) Nat.Struct.Mol.Biol. 11: 777-783

  • DOI: 10.1038/nsmb799
  • Primary Citation of Related Structures:  

  • PubMed 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+)-fr ...

    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.


    Organizational Affiliation

    Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-arginine deiminase type IV
A
670Homo sapiensMutation(s): 0 
Gene 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: 2.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.612α = 90.00
b = 60.437β = 123.61
c = 113.488γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata scaling
CrystalCleardata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance