2XT0

Dehalogenase DPpA from Plesiocystis pacifica SIR-I

Summary for 2XT0

• Entry DOI: 10.2210/pdb2xt0/pdb
• Descriptor: HALOALKANE DEHALOGENASE, SULFATE ION (3 entities in total)
• Functional Keywords: hydrolase, alpha-beta hydrolase fold
• Biological source: PLESIOCYSTIS PACIFICA
• Total number of polymer chains: 1
• Total formula weight: 33008.48

Authors

Bogdanovic, X.,Palm, G.J.,Hinrichs, W. (deposition date: 2010-10-02, release date: 2011-08-10, Last modification date: 2023-12-20)

Primary citation

Hesseler, M.,Bogdanovic, X.,Hidalgo, A.,Berenguer, J.,Palm, G.J.,Hinrichs, W.,Bornscheuer, U.T.
Cloning, Functional Expression, Biochemical Characterization, and Structural Analysis of a Haloalkane Dehalogenase from Plesiocystis Pacifica Sir-1.
Appl.Microbiol.Biotechnol., 91:1049-, 2011

PubMed Abstract: A haloalkane dehalogenase (DppA) from Plesiocystis pacifica SIR-1 was identified by sequence comparison in the NCBI database, cloned, functionally expressed in Escherichia coli, purified, and biochemically characterized. The three-dimensional (3D) structure was determined by X-ray crystallography and has been refined at 1.95 Å resolution to an R-factor of 21.93%. The enzyme is composed of an α/β-hydrolase fold and a cap domain and the overall fold is similar to other known haloalkane dehalogenases. Active site residues were identified as Asp123, His278, and Asp249 and Trp124 and Trp163 as halide-stabilizing residues. DppA, like DhlA from Xanthobacter autotrophicus GJ10, is a member of the haloalkane dehalogenase subfamily HLD-I. As a consequence, these enzymes have in common the relative position of their catalytic residues within the structure and also show some similarities in the substrate specificity. The enzyme shows high preference for 1-bromobutane and does not accept chlorinated alkanes, halo acids, or halo alcohols. It is a monomeric protein with a molecular mass of 32.6 kDa and exhibits maximum activity between 33 and 37°C with a pH optimum between pH 8 and 9. The K(m) and k(cat) values for 1-bromobutane were 24.0 mM and 8.08 s(-1). Furthermore, from the 3D-structure of DppA, it was found that the enzyme possesses a large and open active site pocket. Docking experiments were performed to explain the experimentally determined substrate preferences.

PubMed: 21603934
DOI: 10.1007/S00253-011-3328-X

Experimental method

X-RAY DIFFRACTION (1.9 Å)