Crystal structure of Protein Arginine Deiminase 2 (D123N, 0 mM Ca2+)

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design.

Slade, D.J.Fang, P.Dreyton, C.J.Zhang, Y.Fuhrmann, J.Rempel, D.Bax, B.D.Coonrod, S.A.Lewis, H.D.Guo, M.Gross, M.L.Thompson, P.R.

(2015) ACS Chem Biol 10: 1043-1053

  • DOI: https://doi.org/10.1021/cb500933j
  • Primary Citation of Related Structures:  
    4N20, 4N22, 4N24, 4N25, 4N26, 4N28, 4N2A, 4N2B, 4N2C, 4N2D, 4N2E, 4N2F, 4N2G, 4N2H, 4N2I, 4N2K, 4N2L, 4N2M, 4N2N

  • PubMed Abstract: 

    Protein arginine deiminases (PADs) are calcium-dependent histone-modifying enzymes whose activity is dysregulated in inflammatory diseases and cancer. PAD2 functions as an Estrogen Receptor (ER) coactivator in breast cancer cells via the citrullination of histone tail arginine residues at ER binding sites. Although an attractive therapeutic target, the mechanisms that regulate PAD2 activity are largely unknown, especially the detailed role of how calcium facilitates enzyme activation. To gain insights into these regulatory processes, we determined the first structures of PAD2 (27 in total), and through calcium-titrations by X-ray crystallography, determined the order of binding and affinity for the six calcium ions that bind and activate this enzyme. These structures also identified several PAD2 regulatory elements, including a calcium switch that controls proper positioning of the catalytic cysteine residue, and a novel active site shielding mechanism. Additional biochemical and mass-spectrometry-based hydrogen/deuterium exchange studies support these structural findings. The identification of multiple intermediate calcium-bound structures along the PAD2 activation pathway provides critical insights that will aid the development of allosteric inhibitors targeting the PADs.

  • Organizational Affiliation

    †Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-arginine deiminase type-2690Homo sapiensMutation(s): 1 
Gene Names: PADI2KIAA0994PDI2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2J8 (Homo sapiens)
Explore Q9Y2J8 
Go to UniProtKB:  Q9Y2J8
GTEx:  ENSG00000117115 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2J8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.19α = 90
b = 51.82β = 105.66
c = 75.895γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description