1MJ5

LINB (haloalkane dehalogenase) from sphingomonas paucimobilis UT26 at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.112 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(2004) Biochemistry 43: 870-878

  • DOI: 10.1021/bi034748g

  • PubMed 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-chai ...

    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.


    Related Citations: 
    • Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26
      Marek, J.,Vevodova, J.,Smatanova, I.K.,Nagata, Y.,Svensson, L.A.,Newman, J.,Takagi, M.,Damborsky, J.
      (2000) Biochemistry 39: 14082
    • Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition
      Oakley, A.J.,Prokop, Z.,Bohac, M.,Kmunicek, J.,Jedlicka, T.,Monincova, M.,Kuta-Smatanova, I.,Nagata, Y.,Damborsky, J.,Wilce, M.C.J.
      (2002) Biochemistry 41: 4847


    Organizational Affiliation

    Crystallography Centre, School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase
A
302Sphingomonas paucimobilisGene Names: linB
EC: 3.8.1.5
Find proteins for P51698 (Sphingomonas paucimobilis)
Go to UniProtKB:  P51698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.112 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.390α = 90.00
b = 68.380β = 90.00
c = 80.720γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
SHELXL-97refinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance