1S0Y

The structure of trans-3-chloroacrylic acid dehalogenase, covalently inactivated by the mechanism-based inhibitor 3-bromopropiolate at 2.3 Angstrom resolution

Summary for 1S0Y

• Entry DOI: 10.2210/pdb1s0y/pdb
• Descriptor: alpha-subunit of trans-3-chloroacrylic acid dehalogenase, beta-subunit of trans-3-chloroacrylic acid dehalogenase, MALONIC ACID, ... (4 entities in total)
• Functional Keywords: dehalogenase, tautomerase family, covalent modification, inhibition, michael addition, dehalogenation mechanism, malonyl inhibitor, lyase
• Biological source: Pseudomonas pavonaceae; More
• Total number of polymer chains: 12
• Total formula weight: 97431.17

Authors

de Jong, R.M.,Brugman, W.,Poelarends, G.J.,Whitman, C.P.,Dijkstra, B.W. (deposition date: 2004-01-05, release date: 2004-02-24, Last modification date: 2023-08-23)

Primary citation

de Jong, R.M.,Brugman, W.,Poelarends, G.J.,Whitman, C.P.,Dijkstra, B.W.
The X-ray structure of trans-3-chloroacrylic acid dehalogenase reveals a novel hydration mechanism in the tautomerase superfamily
J.Biol.Chem., 279:11546-11552, 2004

PubMed Abstract: Isomer-specific 3-chloroacrylic acid dehalogenases function in the bacterial degradation of 1,3-dichloropropene, a compound used in agriculture to kill plant-parasitic nematodes. The crystal structure of the heterohexameric trans-3-chloroacrylic acid dehalogenase (CaaD) from Pseudomonas pavonaceae 170 inactivated by 3-bromopropiolate shows that Glu-52 in the alpha-subunit is positioned to function as the water-activating base for the addition of a hydroxyl group to C-3 of 3-chloroacrylate and 3-bromopropiolate, whereas the nearby Pro-1 in the beta-subunit is positioned to provide a proton to C-2. Two arginine residues, alphaArg-8 and alphaArg-11, interact with the C-1 carboxylate groups, thereby polarizing the alpha,beta-unsaturated acids. The reaction with 3-chloroacrylate results in the production of an unstable halohydrin, 3-chloro-3-hydroxypropanoate, which decomposes into the products malonate semialdehyde and HCl. In the inactivation mechanism, however, malonyl bromide is produced, which irreversibly alkylates the betaPro-1. CaaD is related to 4-oxalocrotonate tautomerase, with which it shares an N-terminal proline. However, in 4-oxalocrotonate tautomerase, Pro-1 functions as a base participating in proton transfer within a hydrophobic active site, whereas in CaaD, the acidic proline is stabilized in a hydrophilic active site. The altered active site environment of CaaD thus facilitates a previously unknown reaction in the tautomerase superfamily, the hydration of the alpha,beta-unsaturated bonds of trans-3-chloroacrylate and 3-bromopropiolate. The mechanism for these hydration reactions represents a novel catalytic strategy that results in carbon-halogen bond cleavage.

PubMed: 14701869
DOI: 10.1074/jbc.M311966200

Experimental method

X-RAY DIFFRACTION (2.3 Å)