 |
PDBsum entry 1qq6
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Crystal structures of intermediates in the dehalogenation of haloalkanoates by l-2-Haloacid dehalogenase.
|
|
|
Authors
|
|
I.S.Ridder,
H.J.Rozeboom,
K.H.Kalk,
B.W.Dijkstra.
|
|
|
Ref.
|
|
J Biol Chem, 1999,
274,
30672-30678.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The L-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading bacterium
Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small
L-2-haloalkanoates to their corresponding D-2-hydroxyalkanoates, with inversion
of the configuration at the C(2) atom. The structure of the apoenzyme at pH 8
was refined at 1.5-A resolution. By lowering the pH, the catalytic activity of
the enzyme was considerably reduced, allowing the crystal structure
determination of the complexes with L-2-monochloropropionate and
monochloroacetate at 1.7 and 2.1 A resolution, respectively. Both complexes
showed unambiguous electron density extending from the nucleophile Asp(8) to the
C(2) atom of the dechlorinated substrates corresponding to a covalent
enzyme-ester reaction intermediate. The halide ion that is cleaved off is found
in line with the Asp(8) Odelta1-C(2) bond in a halide-stabilizing cradle made up
of Arg(39), Asn(115), and Phe(175). In both complexes, the Asp(8) Odelta2
carbonyl oxygen atom interacts with Thr(12), Ser(171), and Asn(173), which
possibly constitute the oxyanion hole in the hydrolysis of the ester bond. The
carboxyl moiety of the substrate is held in position by interactions with
Ser(114), Lys(147), and main chain NH groups. The L-2-monochloropropionate CH(3)
group is located in a small pocket formed by side chain atoms of Lys(147),
Asn(173), Phe(175), and Asp(176). The size and position of the pocket explain
the stereospecificity and the limited substrate specificity of the enzyme. These
crystallographic results demonstrate that the reaction of the enzyme proceeds
via the formation of a covalent enzyme-ester intermediate at the nucleophile
Asp(8).
|
|
|
|
|
|
|
|
Figure 2.
Fig. 2. Two conformations of residues 208-213 of
molecules A and B at the dimerization interface.
|
|
Figure 3.
Fig. 3. Schematic representation of the interactions in
the covalent complexes of DhlB with L-2-monochloropropionate (A)
and monochloroacetate (B). Hydrogen bonding interactions with
the covalent intermediate and the chloride ion are represented
by dashed lines, and other interactions are represented by
dotted lines with interatomic distances in Å.
|
|
|
|
|
|
The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1999,
274,
30672-30678)
copyright 1999.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Three-Dimensional structure of l-2-Haloacid dehalogenase from xanthobacter autotrophicus gj10 complexed with the substrate-Analogue formate.
|
|
|
Authors
|
|
I.S.Ridder,
H.J.Rozeboom,
K.H.Kalk,
D.B.Janssen,
B.W.Dijkstra.
|
|
|
Ref.
|
|
J Biol Chem, 1997,
272,
33015-33022.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Figure 3.
Fig. 3. Superimposition of L-2-haloacid dehalogenase monomers
from X. autotrophicus (thick, light shaded lines) and
Pseudomonas sp. YL (thin, darker shaded lines).
|
|
Figure 8.
Fig. 8. Stereo view of the superimposition of dehalogenase
active sites of X. autotrophicus (thick lines) and Pseudomonas
sp. YL (thin lines). The formate ion and water molecules are
shown in ball-and-stick representation.
|
|
|
|
|
|
The above figures are
reproduced from the cited reference
with permission from the ASBMB
|
|
|
Secondary reference #2
|
|
|
Title
|
|
Crystallization and preliminary X-Ray analysis of l-2-Haloacid dehalogenase from xanthobacter autotrophicus gj10.
|
|
|
Authors
|
|
I.S.Ridder,
H.J.Rozeboom,
J.Kingma,
D.B.Janssen,
B.W.Dijkstra.
|
|
|
Ref.
|
|
Protein Sci, 1995,
4,
2619-2620.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
