PDBsum entry 1qq6

Hydrolase

PDB id: 1qq6

Contents

Protein chains

245 a.a. *

Metals

_CL ×2

Waters ×516

* Residue conservation analysis

PDB id:

1qq6

Name:

Hydrolase

Title:

Structure of l-2-haloacid dehalogenase from xanthobacter autotrophicus with chloroacetic acid covalently bound

Structure:

Protein (l-2-haloacid dehalogenase). Chain: a, b. Other_details: chloroacetic acid covalently bound in both active sites

Source:

Xanthobacter autotrophicus. Organism_taxid: 280. Strain: gj10

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.171 R-free: 0.219

Authors:

I.S.Ridder,H.J.Rozeboom,K.H.Kalk,B.W.Dijkstra

Key ref:

I.S.Ridder et al. (1999). Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase. J Biol Chem, 274, 30672-30678. PubMed id: 10521454 DOI: 10.1074/jbc.274.43.30672

Date:

11-Jun-99 Release date: 25-Oct-99

Protein chains

Q60099  (HAD_XANAU) -  (S)-2-haloacid dehalogenase from Xanthobacter autotrophicus

Seq: 253 a.a.

Struc: 245 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.8.1.2 - (S)-2-haloacid dehalogenase.
• Pathway: 2-Haloacid Dehalogenase (configuration-inverting)
• Reaction: an (S)-2-haloacid + H2O = a (2R)-2-hydroxycarboxylate + a halide anion + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.274.43.30672

J Biol Chem 274:30672-30678 (1999)

PubMed id: 10521454

Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase.

I.S.Ridder, H.J.Rozeboom, K.H.Kalk, B.W.Dijkstra.

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).

Selected figure(s)

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.

Figures were selected by the author.