title: Predicting the function of 4-coumarate:CoA ligase (LJ4CL1) in Lonicera japonica.
abstract: 4-Coumarate:CoA ligases (4CLs) are a group of essential enzymes involved in the pathway of phenylpropanoid-derived compound metabolisms; however it is still difficult to identify orthologs and paralogs of these important enzymes just based on sequence similarity of the conserved domains. Using sequence data of 20 plant species from the public databases and sequences from Lonicera japonica, we define 1252 adenosine monophosphate (AMP)-dependent synthetase/ligase sequences and classify them into three phylogenetic clades. 4CLs are in one of the four subgroups, according to their partitioning, with known proteins characterized in A. thaliana and Oryza sativa. We also defined 184 non-redundant sequences that encode proteins containing the GEICIRG motif and the taxonomic distribution of these GEICIRG-containing proteins suggests unique catalytic activities in plants. We further analyzed their transcription levels in L. japonica and L. japonica. var. chinensis flowers and chose the highest expressed genes representing the subgroups for structure and binding site predictions. Coupled with liquid chromatography-mass spectrometry (LC-MS) analysis of the L. japonica flowers, the structural study on putative substrate binding amino acid residues, ferulate, and 4-coumaric acid of the conserved binding-site of LJ4CL1 leads to a conclusion that this highly expressed protein group in the flowers may process 4-coumarate that represents 90% of the known phenylpropanoid-derived compounds. The activity of purified crude LJ4CL1 protein was analyzed using 4-coumarate as template and high activity indicating that 4-coumarate is one of the substrates of LJ4CL1.
authors: State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China. yuanyuan@icmm.ac.cn.
authors: Yuan
authors: Y
authors: Yuan
authors: Pharmacy College, Anhui University of Chinese Medicine, Hefei 230038, China. yushulinss@163.com.
authors: Shulin
authors: S
authors: Yu
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing 100029, China. junyu@big.ac.cn.
authors: Jun
authors: J
authors: Yu
authors: State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China. zzlzhongyi@163.com.
authors: Zhilai
authors: Z
authors: Zhan
authors: State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China. li_minhui@aliyun.com.
authors: Minhui
authors: M
authors: Li
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing 100029, China. liugm@big.ac.cn.
authors: Guiming
authors: G
authors: Liu
authors: CAS Key Laboratory of Genome Sciences and Information, Beijing 100029, China. wangxm@big.ac.cn.
authors: Xumin
authors: X
authors: Wang
authors: State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China. huangluqi@263.net.
authors: Luqi
authors: L
authors: Huang
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D020816:Amino Acid Motifs; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics; D003066:Coenzyme A Ligases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D018628:Gene Dosage; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D031239:Lonicera / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding
chemical_list: D002352:Carrier Proteins; D010940:Plant Proteins; D000255:Adenosine Triphosphate; D003066:Coenzyme A Ligases; C019943:4-coumarate-CoA ligase