3A9V

Crystal structures and enzymatic mechanisms of a Populus tomentosa 4-coumarate--CoA ligase

Summary for 3A9V

• Entry DOI: 10.2210/pdb3a9v/pdb
• Related: 3A9U 3NI2
• Descriptor: 4-coumarate--CoA ligase, ADENOSINE MONOPHOSPHATE (3 entities in total)
• Functional Keywords: 4-coumate--coa ligase, 4cl, phenylpropanoid pathway, ligase
• Biological source: Populus tomentosa (Chinese white poplar)
• Total number of polymer chains: 1
• Total formula weight: 58954.78

Authors

Hu, Y. (deposition date: 2009-11-06, release date: 2010-09-08, Last modification date: 2023-11-01)

Primary citation

Hu, Y.,Gai, Y.,Yin, L.,Wang, X.,Feng, C.,Feng, L.,Li, D.,Jiang, X.N.,Wang, D.C.
Crystal structures of a Populus tomentosa 4-coumarate:CoA ligase shed light on its enzymatic mechanisms
Plant Cell, 22:3093-3104, 2010

PubMed Abstract: 4-Coumaric acid:CoA ligase (4CL) is the central enzyme of the plant-specific phenylpropanoid pathway. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters, the precursors of lignin and other important phenylpropanoids, in two-step reactions involving the formation of hydroxycinnamate-AMP anhydride and then the nucleophilic substitution of AMP by CoA. In this study, we determined the crystal structures of Populus tomentosa 4CL1 in the unmodified (apo) form and in forms complexed with AMP and adenosine 5'-(3-(4-hydroxyphenyl)propyl)phosphate (APP), an intermediate analog, at 2.4, 2.5, and 1.9 Å resolution, respectively. 4CL1 consists of two globular domains connected by a flexible linker region. The larger N-domain contains a substrate binding pocket, while the C-domain contains catalytic residues. Upon binding of APP, the C-domain rotates 81° relative to the N-domain. The crystal structure of 4CL1-APP reveals its substrate binding pocket. We identified residues essential for catalytic activities (Lys-438, Gln-443, and Lys-523) and substrate binding (Tyr-236, Gly-306, Gly-331, Pro-337, and Val-338) based on their crystal structures and by means of mutagenesis and enzymatic activity studies. We also demonstrated that the size of the binding pocket is the most important factor in determining the substrate specificities of 4CL1. These findings shed light on the enzymatic mechanisms of 4CLs and provide a solid foundation for the bioengineering of these enzymes.

PubMed: 20841425
DOI: 10.1105/tpc.109.072652

Experimental method

X-RAY DIFFRACTION (2.5 Å)