PDBsum entry: 1mj5

Hydrolase

PDB id: 1mj5

Contents

Protein chain

298 a.a. *

Metals

_CL ×2

_MG ×3

Waters ×658

* Residue conservation analysis

PDB id:

1mj5

Name:

Hydrolase

Title:

Linb (haloalkane dehalogenase) from sphingomonas paucimobilis ut26 at atomic resolution

Structure:

1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase. Chain: a. Synonym: haloalkane dehalogenase, 1,4- tcdn chlorohydrolase. Engineered: yes

Source:

Sphingomonas paucimobilis. Organism_taxid: 13689. Strain: ut26. Gene: linb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

0.95Å R-factor: 0.112 R-free: 0.141

Authors:

A.J.Oakley,J.Damborsky,M.C.Wilce

Key ref:

A.J.Oakley et al. (2004). Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Biochemistry, 43, 870-878. PubMed id: 14744129

Date:

27-Aug-02 Release date: 27-Aug-03

Protein chain

P51698  (LINB_PSEPA) -  Haloalkane dehalogenase

Seq: 296 a.a.

Struc: 298 a.a.

Enzyme reactions

• Enzyme class: E.C.3.8.1.5 - Haloalkane dehalogenase.
• Reaction: 1-haloalkane + H₂O = a primary alcohol + halide

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

 Gene Ontology (GO) functional annotation 

• Cellular component: periplasmic space (1 term)
• Biological process: response to toxin (1 term)
• Biochemical function: catalytic activity (3 terms)

Added reference

Biochemistry 43:870-878 (2004)

PubMed id: 14744129

Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues.

A.J.Oakley, M.Klvana, M.Otyepka, Y.Nagata, M.C.Wilce, J.Damborský.

ABSTRACT

We present the structure of LinB, a 33-kDa haloalkane dehalogenase from Sphingomonas paucimobilis UT26, at 0.95 A resolution. The data have allowed us to directly observe the anisotropic motions of the catalytic residues. In particular, the side-chain of the catalytic nucleophile, Asp108, displays a high degree of disorder. It has been modeled in two conformations, one similar to that observed previously (conformation A) and one strained (conformation B) that approached the catalytic base (His272). The strain in conformation B was mainly in the C(alpha)-C(beta)-C(gamma) angle (126 degrees ) that deviated by 13.4 degrees from the "ideal" bond angle of 112.6 degrees. On the basis of these observations, we propose a role for the charge state of the catalytic histidine in determining the geometry of the catalytic residues. We hypothesized that double-protonation of the catalytic base (His272) reduces the distance between the side-chain of this residue and that of the Asp108. The results of molecular dynamics simulations were consistent with the structural data showing that protonation of the His272 side-chain nitrogen atoms does indeed reduce the distance between the side-chains of the residues in question, although the simulations failed to demonstrate the same degree of strain in the Asp108 C(alpha)-C(beta)-C(gamma) angle. Instead, the changes in the molecular dynamics structures were distributed over several bond and dihedral angles. Quantum mechanics calculations on LinB with 1-chloro-2,2-dimethylpropane as a substrate were performed to determine which active site conformations and protonation states were most likely to result in catalysis. It was shown that His272 singly protonated at N(delta)(1) and Asp108 in conformation A gave the most exothermic reaction (DeltaH = -22 kcal/mol). With His272 doubly protonated at N(delta)(1) and N(epsilon)(2), the reactions were only slightly exothermic or were endothermic. In all calculations starting with Asp108 in conformation B, the Asp108 C(alpha)-C(beta)-C(gamma) angle changed during the reaction and the Asp108 moved to conformation A. The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB.