Crystal structure of 4-coumarate:CoA ligase complexed with feruloyl adenylate

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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

Li, Z.Nair, S.K.

(2015) Structure 23: 2032-2042

  • DOI: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-coumarate--CoA ligase 2542Nicotiana tabacumMutation(s): 0 
Gene Names: 4CL2
Find proteins for O24146 (Nicotiana tabacum)
Explore O24146 
Go to UniProtKB:  O24146
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO24146
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4UW

Download Ideal Coordinates CCD File 
B [auth A]5'-O-[(R)-hydroxy{[(2E)-3-(5-methoxy-4-oxocyclohexa-1,5-dien-1-yl)prop-2-enoyl]oxy}phosphoryl]adenosine
C20 H22 N5 O10 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.441α = 90
b = 82.441β = 90
c = 181.322γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations