1X42

Crystal structure of a haloacid dehalogenase family protein (PH0459) from Pyrococcus horikoshii OT3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3

Arai, R.Kukimoto-Niino, M.Kuroishi, C.Bessho, Y.Shirouzu, M.Yokoyama, S.

(2006) Protein Sci. 15: 373-377

  • DOI: 10.1110/ps.051922406

  • PubMed Abstract: 
  • PH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 A crystal structure of PH0459 (PDB ID: 1X42) determined by the multiwavelength anom ...

    PH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 A crystal structure of PH0459 (PDB ID: 1X42) determined by the multiwavelength anomalous dispersion method. The core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by six alpha-helices and three 3(10)-helices. One disulfide bond, Cys186-Cys212, forms a bridge between an alpha-helix and a 3(10)-helix, although PH0459 seems to be an intracellular protein. The subdomain inserted into the core domain has a four-helix bundle structure. The crystal packing suggests that PH0459 exists as a monomer. A structural homology search revealed that PH0459 resembles the l-2-haloacid dehalogenases l-DEX YL from Pseudomonas sp. YL and DhlB from Xanthobacter autotrophicus GJ10. A comparison of the active sites suggested that PH0459 probably has haloacid dehalogenase activity, but its substrate specificity may be different. In addition, the disulfide bond in PH0459 probably facilitates the structural stabilization of the neighboring region in the monomeric form, although the corresponding regions in l-DEX YL and DhlB may be stabilized by dimerization. Since heat-stable dehalogenases can be used for the detoxification of halogenated aliphatic compounds, PH0459 will be a useful target for biotechnological research.


    Organizational Affiliation

    Protein Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein PH0459
A
232Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Find proteins for O58216 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O58216
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.113α = 90.00
b = 71.272β = 93.51
c = 53.615γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SOLVEphasing
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance