5BSR

Crystal structure of 4-coumarate:CoA ligase complexed with adenosine monophosphate and Coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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Literature

Structural Basis for Specificity and Flexibility in a Plant 4-Coumarate:CoA Ligase.

Li, Z.Nair, S.K.

(2015) Structure 23: 2032-2042

  • DOI: 10.1016/j.str.2015.08.012
  • Primary Citation of Related Structures:  
    5BSM, 5BSR, 5BST, 5BSU, 5BSV, 5BSW

  • PubMed Abstract: 
  • Plant 4-coumarate:CoA ligase (4CL) serves as a central catalyst in the phenylpropanoid pathway that provides precursors for numerous metabolites and regulates carbon flow. Here, we present several high-resolution crystal structures of Nicotiana tabacum 4CL isoform 2 (Nt4CL2) in complex with Mg(2+) and ATP, with AMP and coenzyme A (CoA), and with three different hydroxycinnamate-AMP intermediates: 4-coumaroyl-AMP, caffeoyl-AMP, and feruloyl-AMP ...

    Plant 4-coumarate:CoA ligase (4CL) serves as a central catalyst in the phenylpropanoid pathway that provides precursors for numerous metabolites and regulates carbon flow. Here, we present several high-resolution crystal structures of Nicotiana tabacum 4CL isoform 2 (Nt4CL2) in complex with Mg(2+) and ATP, with AMP and coenzyme A (CoA), and with three different hydroxycinnamate-AMP intermediates: 4-coumaroyl-AMP, caffeoyl-AMP, and feruloyl-AMP. The Nt4CL2-Mg(2+)-ATP structure is captured in the adenylate-forming conformation, whereas the other structures are in the thioester-forming conformation. These structures represent a rare example of an ANL enzyme visualized in both conformations, and also reveal the binding determinants for both CoA and the hydroxycinnamate substrate. Kinetic studies of structure-based variants were used to identify residues crucial to catalysis, ATP binding, and hydroxycinnamate specificity. Lastly, we characterize a deletion mutant of Nt4CL2 that possesses the unusual sinapinate-utilizing activity. These studies establish a molecular framework for the engineering of this versatile biocatalyst.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Computational Biology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: snair@illinois.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-coumarate--CoA ligase 2A542Nicotiana tabacumMutation(s): 0 
Gene Names: 4CL2
EC: 6.2.1.12
UniProt
Find proteins for O24146 (Nicotiana tabacum)
Explore O24146 
Go to UniProtKB:  O24146
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.898α = 90
b = 82.092β = 90
c = 97.13γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2015-06-02 
  • Released Date: 2016-05-11 
  • Deposition Author(s): Li, Z., Nair, S.K.

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release