4LBI | pdb_00004lbi

5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG) from Burkholderia phenoliruptrix AC1100: Selenomethionyl Apo-form

• PDB DOI: https://doi.org/10.2210/pdb4LBI/pdb

• Classification: LYASE
• Organism(s): Burkholderia cepacia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-20 Released: 2013-08-28 
• Deposition Author(s): Hayes, R.P., Lewis, K.M., Xun, L., Kang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Catalytic Mechanism of 5-Chlorohydroxyhydroquinone Dehydrochlorinase from the YCII Superfamily of Largely Unknown Function.

Hayes, R.P., Lewis, K.M., Xun, L., Kang, C.

(2013) J Biological Chem 288: 28447-28456

• PubMed: 23955343 
• DOI: https://doi.org/10.1074/jbc.M113.499368
• Primary Citation Related Structures: 
  4LBH, 4LBI, 4LBP


• PubMed Abstract: 
  

  TftG, 5-chloro-2-hydroxyhydroquinone (5-CHQ) dehydrochlorinase, is involved in the biodegradation of 2,4,5-trichlorophenoxyacetate by Burkholderia phenoliruptrix AC1100. It belongs to the YCII superfamily, a group of proteins with largely unknown function. In this work, we utilized structural and functional studies, including the apo-form and 2,5-dihydroxybenzoquinone binary complex crystal structures, computational analysis, and site-directed mutagenesis, to determine the dehydrochlorination mechanism. The His-Asp dyad, which initiates catalysis, is strongly conserved in YCII-like proteins. In addition, other catalytically important residues such as Pro-76, which orients the His-Asp catalytic dyad; Arg-17 and Ser-56, which form an oxyanion hole; and Asp-9, which stabilizes the oxyanion hole, are among the most highly conserved residues across the YCII superfamily members. The comprehensive characterization of TftG helps not only for identifying effective mechanisms for chloroaromatic dechlorination but also for understanding the functions of YCII superfamily members, which we propose to be lyases.

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Organizational Affiliation: 
• From the Department of Chemistry and.

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: 45.29 kDa 
• Atom Count: 3,264 
• Modeled Residue Count: 376 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-chloro-2-hydroxyhydroquinone dehydrochlorinase (TftG)	A, B, C, D	100	Burkholderia cepacia	Mutation(s): 0
UniProt
Find proteins for Q45075 (Burkholderia cepacia) Explore Q45075  Go to UniProtKB:  Q45075

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.238	α = 90
b = 158.01	β = 90
c = 50.385	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Hayes, R.P., Lewis, K.M., Xun, L., Kang, C.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2013-10-23
  Changes: Database references
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary