3CZA

Crystal Structure of E18D DJ-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cysteine pKa depression by a protonated glutamic acid in human DJ-1.

Witt, A.C.Lakshminarasimhan, M.Remington, B.C.Hasim, S.Pozharski, E.Wilson, M.A.

(2008) Biochemistry 47: 7430-7440

  • DOI: 10.1021/bi800282d
  • Primary Citation of Related Structures:  2OR3, 3CY6, 3CYF, 3CZ9

  • PubMed Abstract: 
  • Human DJ-1, a disease-associated protein that protects cells from oxidative stress, contains an oxidation-sensitive cysteine (C106) that is essential for its cytoprotective activity. The origin of C106 reactivity is obscure, due in part to the absenc ...

    Human DJ-1, a disease-associated protein that protects cells from oxidative stress, contains an oxidation-sensitive cysteine (C106) that is essential for its cytoprotective activity. The origin of C106 reactivity is obscure, due in part to the absence of an experimentally determined p K a value for this residue. We have used atomic-resolution X-ray crystallography and UV spectroscopy to show that C106 has a depressed p K a of 5.4 +/- 0.1 and that the C106 thiolate accepts a hydrogen bond from a protonated glutamic acid side chain (E18). X-ray crystal structures and cysteine p K a analysis of several site-directed substitutions at residue 18 demonstrate that the protonated carboxylic acid side chain of E18 is required for the maximal stabilization of the C106 thiolate. A nearby arginine residue (R48) participates in a guanidinium stacking interaction with R28 from the other monomer in the DJ-1 dimer and elevates the p K a of C106 by binding an anion that electrostatically suppresses thiol ionization. Our results show that the ionizable residues (E18, R48, and R28) surrounding C106 affect its p K a in a way that is contrary to expectations based on the typical ionization behavior of glutamic acid and arginine. Lastly, a search of the Protein Data Bank (PDB) produces several candidate hydrogen-bonded aspartic/glutamic acid-cysteine interactions, which we propose are particularly common in the DJ-1 superfamily.


    Organizational Affiliation

    Department of Biochemistry and Redox Biology Center, The University of Nebraska, Lincoln, Nebraska 68588-0664, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein DJ-1
A
197Homo sapiensGene Names: PARK7
EC: 3.1.2.-, 3.5.1.-
Find proteins for Q99497 (Homo sapiens)
Go to Gene View: PARK7
Go to UniProtKB:  Q99497
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.131 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.826α = 90.00
b = 74.826β = 90.00
c = 74.777γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
ADSCdata collection
SHELXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-04-29
    Type: Non-polymer description