4N25

Crystal structure of Protein Arginine Deiminase 2 (250 uM Ca2+)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1021/cb500933j
  • Primary Citation of Related Structures:  
    4N20, 4N22, 4N24, 4N25, 4N26, 4N2H, 4N2I, 4N2K, 4N2L, 4N2M

  • 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 ...

    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 Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein-arginine deiminase type-2A690Homo sapiensMutation(s): 0 
Gene Names: PADI2KIAA0994PDI2PAD2
EC: 3.5.3.15
Find proteins for Q9Y2J8 (Homo sapiens)
Explore Q9Y2J8 
Go to UniProtKB:  Q9Y2J8
NIH Common Fund Data Resources
PHAROS:  Q9Y2J8
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.276α = 90
b = 51.536β = 105.56
c = 75.992γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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