Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.26 kDa 
• Atom Count: 2763 
• Modelled Residue Count: 310 
• Deposited Residue Count: 310 
• Unique protein chains: 1

1BEZ

HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR AT PH 5

• DOI: 10.2210/pdb1BEZ/pdb

• Classification: DEHALOGENASE
• Organism(s): Xanthobacter autotrophicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-05-18 Released: 1998-11-11 
• Deposition Author(s): Ridder, I.S., Vos, G.J., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 

Literature

Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site.

Krooshof, G.H., Ridder, I.S., Tepper, A.W., Vos, G.J., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W., Janssen, D.B.

(1998) Biochemistry 37: 15013-15023

• PubMed: 9790663 
• DOI: 10.1021/bi9815187
• Primary Citation of Related Structures:  
  1BE0, 1BEE, 1BEZ


• PubMed Abstract: 
  

Haloalkane dehalogenase (DhlA) catalyzes the hydrolysis of haloalkanes via an alkyl-enzyme intermediate. Trp175 forms a halogen/halide-binding site in the active-site cavity together with Trp125. To get more insight in the role of Trp175 in DhlA, we mutated residue 175 and explored the kinetics and X-ray structure of the Trp175Tyr enzyme. The mutagenesis study indicated that an aromatic residue at position 175 is important for the catalytic performance of DhlA. Pre-steady-state kinetic analysis of Trp175Tyr-DhlA showed that the observed 6-fold increase of the Km for 1,2-dibromoethane (DBE) results from reduced rates of both DBE binding and cleavage of the carbon-bromine bond. Furthermore, the enzyme isomerization preceding bromide release became 4-fold faster in the mutant enzyme. As a result, the rate of hydrolysis of the alkyl-enzyme intermediate became the main determinant of the kcat for DBE, which was 2-fold higher than the wild-type kcat. The X-ray structure of the mutant enzyme at pH 6 showed that the backbone structure of the enzyme remains intact and that the tyrosine side chain lies in the same plane as Trp175 in the wild-type enzyme. The Clalpha-stabilizing aromatic rings of Tyr175 and Trp125 are 0.7 A further apart and due to the smaller size of the mutated residue, the volume of the cavity has increased by one-fifth. X-ray structures of mutant and wild-type enzyme at pH 5 demonstrated that the Tyr175 side chain rotated away upon binding of an acetic acid molecule, leaving one of its oxygen atoms hydrogen bonded to the indole nitrogen of Trp125 only. These structural changes indicate a weakened interaction between residue 175 and the halogen atom or halide ion in the active site and help to explain the kinetic changes induced by the Trp175Tyr mutation.

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Related Citations: 

• Crystallographic Analysis of the Catalytic Mechanism of Haloalkane Dehalogenase
  Verschueren, K.H., Seljee, F., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.
  (1993) Nature 363: 693

• Refined X-Ray Structures of Haloalkane Dehalogenase at Ph 6.2 And Ph 8.2 And Implications for the Reaction Mechanism
  Verschueren, K.H., Franken, S.M., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.
  (1993) J Mol Biol 232: 856

• Crystal Structure of Haloalkane Dehalogenase: An Enzyme to Detoxify Halogenated Alkanes
  Franken, S.M., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.
  (1991) EMBO J 10: 1297

• Crystallization of Haloalkane Dehalogenase from Xanthobacter Autotrophicus Gj10
  Rozeboom, H.J., Kingma, J., Janssen, D.B., Dijkstra, B.W.
  (1988) J Mol Biol 200: 611

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Organizational Affiliation: 

Laboratory of Biochemistry, BIOSON Research Institute, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HALOALKANE DEHALOGENASE	A	310	Xanthobacter autotrophicus	Mutation(s): 1  Gene Names: dhlA EC: 3.8.1.5
UniProt
Find proteins for P22643 (Xanthobacter autotrophicus) Explore P22643  Go to UniProtKB:  P22643

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	B [auth A], C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.225 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.03	α = 90
b = 72.3	β = 90
c = 40.96	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
BIOMOL	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-05-18 
• Released Date: 1998-11-11 
Deposition Author(s): Ridder, I.S., Vos, G.J., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.

Revision History  

• Version 1.0: 1998-11-11
  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: 2018-04-18
  Changes: Data collection, Other