H.R. Novak et al. / FEBS Letters 588 (2014) 1616–1622
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the substrate in the correct orientation by stabilizing both the tran-
2.2. Enzyme activity
sition state and the halide ion released during the carbon–carbon
bond break. The division of HLDs into three phylogenetic subfam-
ilies was defined by Chovancova et al. in 2007 [14], depending on
the amino acid content of the catalytic pentad. Classification of
these HLDs into four groups based on substrate specificity revealed
there was no clear correlation between substrate specificity and
phylogenetic subfamilies [15]. More recently, the characterisation
of a HLD from Agrobacterium tumefaciens that has a unique
halide-stabilizing tyrosine residue (Tyr109) in place of the con-
served Trp residue [16] has required an extension of the existing
phylogenetic families.
The HLD activity was measured using a modified colorimetric
assay, based on the method of Holloway et al. [23]. The assay solu-
tion had a final concentration of 1 mM HEPES, 1 mM EDTA, 20 mM
sodium sulfate, 10 mM substrate, 20
initiate the assay, 180 l of dehalogenase assay solution was mixed
with 20 l of purified protein (2 mg/ml). The reaction was followed
lg/ml phenol red, pH 8.2. To
l
l
by measuring a decrease in absorbance at 540 nm over 1 h. To pro-
duce a standard curve, the dehalogenase assay solution was mixed
with HCl to a final concentration between 0 and 2 mM in a total
volume of 200 ll.
Over the last decade the marine environment has been recogni-
sed as a potential source of novel enzymes [17]. The oceans are
known to contain abundant organohalogens, which are thought
to be produced mainly by marine algae. Some species of polychaete
tube worms also produce a wide range of structurally diverse hal-
ogenated compounds [18]. These compounds are often cytotoxic
and are thought to be part of the organism’s defence mechanisms.
Microorganisms living in symbiosis with algae and tube worms
may have evolved detoxification enzymes such as dehalogenases.
In the search of novel dehalogenase enzymes, a marine Rhodob-
acteraceae species was isolated from the surface of a tube worm.
2.3. Crystallization
The purified HanR enzyme was concentrated until a final con-
centration of 10 mg/ml was reached. The concentrated protein
was subjected to microbatch crystallization screens at 18 °C using
an Oryx Robot (Douglas Instruments). The best crystals were
grown from a mixture of equal volumes of protein and precipitant
solution containing 0.15 M MgCl2, 0.1 M Tris–HCl and 15% PEG
4000, pH 8.0. The native crystals were frozen using a cryoprotec-
tant containing 0.1 M Tris–HCl pH 8.0, 0.1 M NaCl, 25% PEG 4000
and 30% PEG 400. The substrate soak was conducted by soaking
the HanR crystal for 1 min in 0.1 M Tris–HCl, 20% PEG 3350, 30%
PEG 400, 25 mM 1-bromohexane, pH 4.0.
The wild-type bacterium tested positive for
L-haloacid dehalogen-
ase ( -HAD) activity. In order to obtain sufficient quantities of this
L
enzyme for biochemical characterisation, the Rhodobacteraceae
genome was partially sequenced so that the gene could be cloned
and the protein over-expressed [19]. In addition to the presence of
2.4. Data collection and structure determination
a novel L-HAD which has been biochemically and structurally char-
acterised [19], a putative HLD was also identified called HanR.
This paper describes the biochemical and structural character-
isation of a HLD enzyme from a marine source which has been
isolated from the surface of a tube worm.
Diffraction data were collected at the Diamond Light Source
synchrotron, UK. Data were processed and scaled with the pro-
grams XDS [24] and Aimless [25] using the Xia2 [26] pipeline. Fur-
ther data analysis and refinement were performed using the CCP4
suite of programs [27].
2. Material and methods
The HanR native structure was solved by molecular replace-
ment (MR) with the program MOLREP [28] using the LinB model
(PDB: 1CV2; [6]). The MR solution was submitted to an automated
refinement procedure using ARP/wARP version 7.0.1 [29]. The
resulting model was manually rebuilt in COOT [30] and refined
with REFMAC5 [31].
The structure of the product bound 1-hexanol (1HO) complex
was solved by MR using the refined structure of the native HanR.
The dictionary definition for the ligand was built using JLIGAND
[32]. The quality of the structures was checked using the program
PROCHECK [33]. The program PyMOL [34] was used to produce
Figs. 2a, 3 and 4.
2.1. Gene identification, cloning and overexpression
A Rhodobacteraceae family bacterium (Rhb) isolated from a
Polychaeta worm was collected from Tralee beach, Argyll, UK.
The Rhb genomic DNA was extracted and the genome was
sequenced using an Illumina GA2 sequencer. As there was low gen-
ome identity to previously sequenced genomes, De novo assembly
was used to arrange the 72 bp paired-end reads into 1082 contigs
using Velvet, version 0.7.63 [20]. A preliminary genome of 3.77
Mbp was assembled into 795 contigs. A putative HLD gene called
HanR was identified using the NCBI BLAST tool [21] on a Galaxy
bioinformatics pipeline [22]. The HanR gene was cloned from geno-
mic DNA into the pET-28a plasmid with a N-terminal His-tag. The
HanR protein was over-expressed in BL21-CodonPlus (DE3) Roset-
ta2 Escherichia coli.
3. Results and discussion
3.1. Biochemical characterisation
The cell pellet was re-suspended in buffer A (0.1 M Tris–HCl,
0.1 M NaCl, 0.5 mM EDTA, 1 mM BAM, 1 mM PMSF, pH 8.2) con-
taining 0.01 M imidazole, lysed by sonication and centrifuged to
remove cell debris. A nickel affinity chromatography column (GE
Healthcare) was equilibrated with buffer A, the cell extract loaded
and the unbound protein washed off with buffer A containing
0.01 M imidazole. The bound protein was eluted in buffer A with
0.5 M imidazole.
The fractions corresponding to the protein were concentrated
using a 10 kDa membrane (Vivaspin 20, Vivascience) at 3000Âg,
at 4 °C until the final volume reached 1 ml. The concentrated pro-
tein sample was further purified on a 120 ml Superdex 75 GF chro-
matography column which was eluted over 1 column volume of
buffer A.
The specific activity of the HanR was measured with a variety of
substrates (Fig. 1). The HanR is active towards both chloroalkanes
and bromoalkanes with preference towards longer chain linear
substrates.
Activity of HanR towards brominated compounds appears to be
higher than towards their chlorinated equivalents, which is not
surprising, as the energy of C–Br bond is lower than that of C–Cl.
This is also in line with the abundance of brominated organic com-
pounds in the marine environment. The DppA HLD from the mar-
ine bacteria Plesiocystis pacifica [11] is not active towards any
chlorinated compounds. Substrate variations between the HLD en-
zymes are thought to arise from differences in the size, shape and
hydrophobicity of the cap domain [14]. The differences in substrate
specificity are difficult to infer from protein sequence only.