3TEA

Crystal structure of Arthrobacter sp. strain su 4-hydroxybenzoyl CoA thioesterase double mutant Q58E/E73A complexed with 4-hydroxyphenacyl CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


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Literature

The Catalytic Mechanism of the Hotdog-fold Enzyme Superfamily 4-Hydroxybenzoyl-CoA Thioesterase from Arthrobacter sp. Strain SU.

Song, F.Thoden, J.B.Zhuang, Z.Latham, J.Trujillo, M.Holden, H.M.Dunaway-Mariano, D.

(2012) Biochemistry 51: 7000-7016

  • DOI: https://doi.org/10.1021/bi301059m
  • Primary Citation of Related Structures:  
    3R32, 3R34, 3R35, 3R36, 3R37, 3R3A, 3R3B, 3R3C, 3R3D, 3R3F, 3TEA

  • PubMed Abstract: 

    The hotdog-fold enzyme 4-hydroxybenzoyl-coenzyme A (4-HB-CoA) thioesterase from Arthrobacter sp. strain AU catalyzes the hydrolysis of 4-HB-CoA to form 4-hydroxybenzoate (4-HB) and coenzyme A (CoA) in the final step of the 4-chlorobenzoate dehalogenation pathway. Guided by the published X-ray structures of the liganded enzyme (Thoden, J. B., Zhuang, Z., Dunaway-Mariano, D., and Holden H. M. (2003) J. Biol. Chem. 278, 43709-43716), a series of site-directed mutants were prepared for testing the roles of active site residues in substrate binding and catalysis. The mutant thioesterases were subjected to X-ray structure determination to confirm retention of the native fold, and in some cases, to reveal changes in the active site configuration. In parallel, the wild-type and mutant thioesterases were subjected to transient and steady-state kinetic analysis, and to (18)O-solvent labeling experiments. Evidence is provided that suggests that Glu73 functions in nucleophilic catalysis, that Gly65 and Gln58 contribute to transition-state stabilization via hydrogen bond formation with the thioester moiety and that Thr77 orients the water nucleophile for attack at the 4-hydroxybenzoyl carbon of the enzyme-anhydride intermediate. The replacement of Glu73 with Asp was shown to switch the function of the carboxylate residue from nucleophilic catalysis to base catalysis and thus, the reaction from a two-step process involving a covalent enzyme intermediate to a single-step hydrolysis reaction. The E73D/T77A double mutant regained most of the catalytic efficiency lost in the E73D single mutant. The results from (31)P NMR experiments indicate that the substrate nucleotide unit is bound to the enzyme surface. Kinetic analysis of site-directed mutants was carried out to determine the contributions made by Arg102, Arg150, Ser120, and Thr121 in binding the nucleotide unit. Lastly, we show by kinetic and X-ray analyses of Asp31, His64, and Glu78 site-directed mutants that these three active site residues are important for productive binding of the substrate 4-hydroxybenzoyl ring.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxybenzoyl-CoA thioesterase
A, B
151Arthrobacter sp.Mutation(s): 2 
Gene Names: fcbCfcbC1
EC: 3.1.2.23
UniProt
Find proteins for Q04416 (Arthrobacter sp)
Explore Q04416 
Go to UniProtKB:  Q04416
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04416
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4CO
Query on 4CO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
4-HYDROXYPHENACYL COENZYME A
C29 H42 N7 O18 P3 S
ZQLMPRRTUJBILA-VXAHOBLNSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4CO Binding MOAD:  3TEA Kd: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.8α = 90
b = 112.8β = 90
c = 60.9γ = 120
Software Package:
Software NamePurpose
FRAMBOdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SAINTdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-08-29
    Changes: Database references
  • Version 1.2: 2012-09-19
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description