4N2G

Crystal structure of Protein Arginine Deiminase 2 (D169A, 10 mM Ca2+)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 

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:  

  • 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 citrullinati ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-arginine deiminase type-2
A
690Homo sapiensMutation(s): 1 
Gene Names: PADI2 (KIAA0994, PAD2, PDI2)
EC: 3.5.3.15
Find proteins for Q9Y2J8 (Homo sapiens)
Go to Gene View: PADI2
Go to UniProtKB:  Q9Y2J8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD
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Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 204.450α = 90.00
b = 50.940β = 105.98
c = 75.940γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
MAR345dtbdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references