1PX0 | pdb_00001px0

Crystal structure of the haloalcohol dehalogenase HheC complexed with the haloalcohol mimic (R)-1-para-nitro-phenyl-2-azido-ethanol

• PDB DOI: https://doi.org/10.2210/pdb1PX0/pdb

• Classification: LYASE
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-07-02 Released: 2003-10-07 
• Deposition Author(s): de Jong, R.M., Tiesinga, J.J.W., Rozeboom, H.J., Kalk, K.H., Tang, L., Janssen, D.B., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure and Mechanism of a Bacterial Haloalcohol Dehalogenase: a new variation of the short-chain dehydrogenase/reductase fold without an NAD(P)H binding site

de Jong, R.M., Tiesinga, J.J.W., Rozeboom, H.J., Kalk, K.H., Tang, L., Janssen, D.B., Dijkstra, B.W.

(2003) EMBO J 22: 4933-4944

• PubMed: 14517233 
• DOI: https://doi.org/10.1093/emboj/cdg479
• Primary Citation Related Structures: 
  1PWX, 1PWZ, 1PX0


• PubMed Abstract: 
  

  Haloalcohol dehalogenases are bacterial enzymes that catalyze the cofactor-independent dehalogenation of vicinal haloalcohols such as the genotoxic environmental pollutant 1,3-dichloro-2-propanol, thereby producing an epoxide, a chloride ion and a proton. Here we present X-ray structures of the haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1, and complexes of the enzyme with an epoxide product and chloride ion, and with a bound haloalcohol substrate mimic. These structures support a catalytic mechanism in which Tyr145 of a Ser-Tyr-Arg catalytic triad deprotonates the haloalcohol hydroxyl function to generate an intramolecular nucleophile that substitutes the vicinal halogen. Haloalcohol dehalogenases are related to the widespread family of NAD(P)H-dependent short-chain dehydrogenases/reductases (SDR family), which use a similar Ser-Tyr-Lys/Arg catalytic triad to catalyze reductive or oxidative conversions of various secondary alcohols and ketones. Our results reveal the first structural details of an SDR-related enzyme that catalyzes a substitutive dehalogenation reaction rather than a redox reaction, in which a halide-binding site is found at the location of the NAD(P)H binding site. Structure-based sequence analysis reveals that the various haloalcohol dehalogenases have likely originated from at least two different NAD-binding SDR precursors.

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Organizational Affiliation: 
• Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 112.75 kDa 
• Atom Count: 8,630 
• Modeled Residue Count: 1,008 
• Deposited Residue Count: 1,016 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
halohydrin dehalogenase	A, B, C, D	254	Agrobacterium tumefaciens	Mutation(s): 0
UniProt
Find proteins for Q93D82 (Agrobacterium tumefaciens) Explore Q93D82  Go to UniProtKB:  Q93D82

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RPN	E [auth A], F [auth B], G [auth C], H [auth D]	(R)-1-PARA-NITRO-PHENYL-2-AZIDO-ETHANOL C8 H8 N4 O3 DHEGJYKMZJGYGW-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.703	α = 90
b = 71.843	β = 92.82
c = 97.31	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-07 
Deposition Author(s): de Jong, R.M., Tiesinga, J.J.W., Rozeboom, H.J., Kalk, K.H., Tang, L., Janssen, D.B., Dijkstra, B.W.

Revision History  

• Version 1.0: 2003-10-07
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description