Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21005.19 
• Atom Count: 1424 
• Residue Count: 197 
• Unique protein chains: 1

3CYF

Crystal Structure of E18N DJ-1

• DOI: 10.2210/pdb3CYF/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2008-04-25 Released: 2008-07-01 
• Deposition Author(s): Witt, A.C., Lakshminarasimhan, M., Remington, B.C., Hasim, S., Pozharski, E., Wilson, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.184 
• R-Value Work: 0.158 

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

• PubMed: 18570440 
• DOI: 10.1021/bi800282d
• Primary Citation of Related Structures:  
  3CZA, 3CZ9, 3CY6, 2OR3


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Protein DJ-1	A	197	Homo sapiens	Mutation(s): 1  Gene Names: PARK7 EC: 3.1.2.-, 3.5.1.-, 3.5.1.124
Find proteins for Q99497 (Homo sapiens) Go to Gene View: PARK7 Go to UniProtKB:  Q99497

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.184 
• R-Value Work: 0.158 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 75.025	α = 90.00
b = 75.025	β = 90.00
c = 75.054	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
HKL-2000	data reduction
PHASER	phasing
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-04-25 
• Released Date: 2008-07-01 
• Deposition Author(s): Witt, A.C., Lakshminarasimhan, M., Remington, B.C., Hasim, S., Pozharski, E., Wilson, M.A.

Revision History 

• Version 1.0: 2008-07-01
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2014-11-12
  Type: Other