1D07

Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 with 1,3-propanediol, a product of debromidation of dibrompropane, at 2.0A resolution

Summary for 1D07

• Entry DOI: 10.2210/pdb1d07/pdb
• Related: 1CV2
• Descriptor: HALOALKANE DEHALOGENASE, BROMIDE ION, 1,3-PROPANDIOL, ... (4 entities in total)
• Functional Keywords: dehalogenase, lindane, biodegradation, alpha/beta-hydrolase, hydrolase
• Biological source: Sphingomonas paucimobilis
• Cellular location: Periplasm : P51698
• Total number of polymer chains: 1
• Total formula weight: 33380.51

Authors

Marek, J.,Vevodova, J.,Damborsky, J.,Smatanova, I.,Svensson, L.A.,Newman, J.,Nagata, Y.,Takagi, M. (deposition date: 1999-09-09, release date: 2000-09-11, Last modification date: 2023-08-09)

Primary citation

Marek, J.,Vevodova, J.,Smatanova, I.K.,Nagata, Y.,Svensson, L.A.,Newman, J.,Takagi, M.,Damborsky, J.
Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26.
Biochemistry, 39:14082-14086, 2000

PubMed Abstract: The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. Here, we present the 1.58 A crystal structure of LinB and the 2.0 A structure of LinB with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. The enzyme belongs to the alpha/beta hydrolase family and contains a catalytic triad (Asp108, His272, and Glu132) in the lipase-like topological arrangement previously proposed from mutagenesis experiments. The LinB structure was compared with the structures of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 and from Rhodococcus sp. and the structural features involved in the adaptation toward xenobiotic substrates were identified. The arrangement and composition of the alpha-helices in the cap domain results in the differences in the size and shape of the active-site cavity and the entrance tunnel. This is the major determinant of the substrate specificity of this haloalkane dehalogenase.

PubMed: 11087355
DOI: 10.1021/bi001539c

Experimental method

X-RAY DIFFRACTION (2 Å)