Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

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This is version 1.3 of the entry. See complete history


Haloalkane dehalogenases: structure of a Rhodococcus enzyme.

Newman, J.Peat, T.S.Richard, R.Kan, L.Swanson, P.E.Affholter, J.A.Holmes, I.H.Schindler, J.F.Unkefer, C.J.Terwilliger, T.C.

(1999) Biochemistry 38: 16105-16114

  • DOI: https://doi.org/10.1021/bi9913855
  • Primary Citation of Related Structures:  
    1BN6, 1BN7, 1CQW

  • PubMed Abstract: 

    The hydrolytic haloalkane dehalogenases are promising bioremediation and biocatalytic agents. Two general classes of dehalogenases have been reported from Xanthobacter and Rhodococcus. While these enzymes share 30% amino acid sequence identity, they have significantly different substrate specificities and halide-binding properties. We report the 1.5 A resolution crystal structure of the Rhodococcus dehalogenase at pH 5.5, pH 7.0, and pH 5.5 in the presence of NaI. The Rhodococcus and Xanthobacter enzymes have significant structural homology in the alpha/beta hydrolase core, but differ considerably in the cap domain. Consistent with its broad specificity for primary, secondary, and cyclic haloalkanes, the Rhodococcus enzyme has a substantially larger active site cavity. Significantly, the Rhodococcus dehalogenase has a different catalytic triad topology than the Xanthobacter enzyme. In the Xanthobacter dehalogenase, the third carboxylate functionality in the triad is provided by D260, which is positioned on the loop between beta7 and the penultimate helix. The carboxylate functionality in the Rhodococcus catalytic triad is donated from E141. A model of the enzyme cocrystallized with sodium iodide shows two iodide binding sites; one that defines the normal substrate and product-binding site and a second within the active site region. In the substrate and product complexes, the halogen binds to the Xanthobacter enzyme via hydrogen bonds with the N(eta)H of both W125 and W175. The Rhodococcusenzyme does not have a tryptophan analogous to W175. Instead, bound halide is stabilized with hydrogen bonds to the N(eta)H of W118 and to N(delta)H of N52. It appears that when cocrystallized with NaI the Rhodococcus enzyme has a rare stable S-I covalent bond to S(gamma) of C187.

  • Organizational Affiliation

    Life Sciences Division, Los Alamos National Laboratory, New Mexico. janet@stromix.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HALOALKANE DEHALOGENASE294Rhodococcus sp. (in: high G+C Gram-positive bacteria)Mutation(s): 0 
Find proteins for P59336 (Rhodococcus sp. (strain TDTM0003))
Explore P59336 
Go to UniProtKB:  P59336
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59336
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ACT

Download Ideal Coordinates CCD File 
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.63α = 90
b = 79.89β = 90
c = 42.93γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations