3CZA

Crystal Structure of E18D DJ-1

Summary for 3CZA

• Entry DOI: 10.2210/pdb3cza/pdb
• Related: 1P5F 2OR3 3CY6 3CYF 3CZ9
• Descriptor: Protein DJ-1, MALONIC ACID (3 entities in total)
• Functional Keywords: reactive cysteine, chaperone, nucleus, oncogene, oxidation, parkinson disease, unknown function
• Biological source: Homo sapiens (Human)
• Cellular location: Cell membrane ; Lipid-anchor : Q99497
• Total number of polymer chains: 1
• Total formula weight: 21078.24

Authors

Witt, A.C.,Lakshminarasimhan, M.,Remington, B.C.,Hashim, S.,Pozharski, E.,Wilson, M.A. (deposition date: 2008-04-28, release date: 2008-07-01, Last modification date: 2023-08-30)

Primary citation

Witt, A.C.,Lakshminarasimhan, M.,Remington, B.C.,Hasim, S.,Pozharski, E.,Wilson, M.A.
Cysteine pKa depression by a protonated glutamic acid in human DJ-1.
Biochemistry, 47:7430-7440, 2008

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.

PubMed: 18570440
DOI: 10.1021/bi800282d

Experimental method

X-RAY DIFFRACTION (1.2 Å)