4CL3_ORYSJ
ID 4CL3_ORYSJ Reviewed; 554 AA.
AC Q6ETN3;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=4-coumarate--CoA ligase 3 {ECO:0000303|PubMed:18627494};
DE Short=4CL 3 {ECO:0000303|PubMed:18627494};
DE Short=Os4CL3 {ECO:0000303|PubMed:18627494};
DE EC=6.2.1.12 {ECO:0000269|PubMed:21807887, ECO:0000269|PubMed:23246835};
DE AltName: Full=4-coumaroyl-CoA synthase 3 {ECO:0000305};
GN Name=4CL3 {ECO:0000303|PubMed:18627494};
GN OrderedLocusNames=Os02g0177600 {ECO:0000312|EMBL:BAF07983.1},
GN LOC_Os02g08100 {ECO:0000305};
GN ORFNames=OsJ_005431 {ECO:0000312|EMBL:EAZ21948.1},
GN P0504A05.24 {ECO:0000312|EMBL:BAD27987.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Fujiminori;
RA Nakano Y., Satoh K., Mase K., Nishikubo N., Kitano H., Katayama Y.;
RT "4-coumarate:CoA ligase in Rice.";
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP GENE FAMILY.
RX PubMed=18627494; DOI=10.1111/j.1469-8137.2008.02534.x;
RA de Azevedo Souza C., Barbazuk B., Ralph S.G., Bohlmann J., Hamberger B.,
RA Douglas C.J.;
RT "Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase
RT (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella.";
RL New Phytol. 179:987-1003(2008).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND TISSUE
RP SPECIFICITY.
RX PubMed=21807887; DOI=10.1104/pp.111.178301;
RA Gui J., Shen J., Li L.;
RT "Functional characterization of evolutionarily divergent 4-
RT coumarate:coenzyme a ligases in rice.";
RL Plant Physiol. 157:574-586(2011).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND INDUCTION.
RX PubMed=23246835; DOI=10.1016/j.bbrc.2012.12.019;
RA Sun H., Li Y., Feng S., Zou W., Guo K., Fan C., Si S., Peng L.;
RT "Analysis of five rice 4-coumarate:coenzyme A ligase enzyme activity and
RT stress response for potential roles in lignin and flavonoid biosynthesis in
RT rice.";
RL Biochem. Biophys. Res. Commun. 430:1151-1156(2013).
CC -!- FUNCTION: Involved in the phenylpropanoid metabolism by mediating the
CC activation of a number of hydroxycinnamates for the biosynthesis of
CC monolignols and other phenolic secondary metabolites (PubMed:21807887,
CC PubMed:23246835). Catalyzes the formation of CoA esters of cinnamate,
CC 4-coumarate, caffeate and ferulate (PubMed:21807887, PubMed:23246835).
CC Is more efficient with substrates in the following order: ferulate > 4-
CC coumarate > caffeate > cinnamate (PubMed:21807887). Possesses very high
CC activity compared to 4CL1, 4CL2, 4CL4 and 4CL5 (PubMed:21807887).
CC Cannot convert sinapate to its corresponding CoA ester
CC (PubMed:21807887, PubMed:23246835). May play a role in the synthesis of
CC lignin as well as other phenolic compounds (PubMed:21807887).
CC {ECO:0000269|PubMed:21807887, ECO:0000269|PubMed:23246835}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(E)-4-coumarate + ATP + CoA = (E)-4-coumaroyl-CoA + AMP +
CC diphosphate; Xref=Rhea:RHEA:19641, ChEBI:CHEBI:12876,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:85008, ChEBI:CHEBI:456215; EC=6.2.1.12;
CC Evidence={ECO:0000269|PubMed:21807887, ECO:0000269|PubMed:23246835};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:19642;
CC Evidence={ECO:0000269|PubMed:21807887, ECO:0000269|PubMed:23246835};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=28.2 uM for cinnamate {ECO:0000269|PubMed:21807887};
CC KM=4.9 uM for 4-coumarate {ECO:0000269|PubMed:21807887};
CC KM=10.9 uM for caffeate {ECO:0000269|PubMed:21807887};
CC KM=3.5 uM for ferulate {ECO:0000269|PubMed:21807887};
CC Vmax=3.01 nmol/sec/mg enzyme with cinnamate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=4.7 nmol/sec/mg enzyme with 4-coumarate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=4.21 nmol/sec/mg enzyme with caffeate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=4.93 nmol/sec/mg enzyme with ferulate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Note=kcat is 10.92 min(-1) with cinnamate as substrate
CC (PubMed:21807887). kcat is 17.1 min(-1) with 4-coumarate as substrate
CC (PubMed:21807887). kcat is 15.3 min(-1) with caffeate as substrate
CC (PubMed:21807887). kcat is 17.94 min(-1) with ferulate as substrate
CC (PubMed:21807887). {ECO:0000269|PubMed:21807887};
CC -!- PATHWAY: Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene
CC biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step
CC 1/2. {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in root exodermis and epidermis cells,
CC stem vascular cells, leaf developing vascular bundle cells and
CC parenchyma cells, lemma, palea, stamens and pistil.
CC {ECO:0000269|PubMed:21807887}.
CC -!- INDUCTION: Induced by wounding (PubMed:23246835). Down-regulated by UV
CC irradiation (PubMed:23246835). {ECO:0000269|PubMed:23246835}.
CC -!- DOMAIN: Both substrate-binding domains (SBD1 and SBD2) are involved in
CC the substrate recognition, and are sufficient to confer the substrate
CC specificity. {ECO:0000250|UniProtKB:Q42524}.
CC -!- MISCELLANEOUS: Plants silencing 4CL3 exhibit significant lignin
CC reduction, reduced plant height, decreased panicle fertility and
CC abnormal anther development. {ECO:0000269|PubMed:21807887}.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
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DR EMBL; AB234050; BAF30962.1; -; mRNA.
DR EMBL; AP004838; BAD27987.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF07983.1; -; Genomic_DNA.
DR EMBL; AP014958; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CM000139; EAZ21948.1; -; Genomic_DNA.
DR RefSeq; XP_015625716.1; XM_015770230.1.
DR AlphaFoldDB; Q6ETN3; -.
DR SMR; Q6ETN3; -.
DR STRING; 4530.OS02T0177600-01; -.
DR PaxDb; Q6ETN3; -.
DR PRIDE; Q6ETN3; -.
DR EnsemblPlants; Os02t0177600-01; Os02t0177600-01; Os02g0177600.
DR GeneID; 4328485; -.
DR Gramene; Os02t0177600-01; Os02t0177600-01; Os02g0177600.
DR KEGG; osa:4328485; -.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q6ETN3; -.
DR OrthoDB; 683933at2759; -.
DR BRENDA; 6.2.1.12; 4460.
DR PlantReactome; R-OSA-1119316; Phenylpropanoid biosynthesis.
DR PlantReactome; R-OSA-1119531; Flavonoid biosynthesis.
DR UniPathway; UPA00372; UER00547.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000007752; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR Genevisible; Q6ETN3; OS.
DR GO; GO:0016207; F:4-coumarate-CoA ligase activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016405; F:CoA-ligase activity; IBA:GO_Central.
DR GO; GO:0106290; F:trans-cinnamate-CoA ligase activity; IDA:UniProtKB.
DR GO; GO:0009698; P:phenylpropanoid metabolic process; IDA:UniProtKB.
DR Gene3D; 3.30.300.30; -; 1.
DR Gene3D; 3.40.50.12780; -; 1.
DR InterPro; IPR025110; AMP-bd_C.
DR InterPro; IPR045851; AMP-bd_C_sf.
DR InterPro; IPR020845; AMP-binding_CS.
DR InterPro; IPR000873; AMP-dep_Synth/Lig.
DR InterPro; IPR042099; ANL_N_sf.
DR Pfam; PF00501; AMP-binding; 1.
DR Pfam; PF13193; AMP-binding_C; 1.
DR PROSITE; PS00455; AMP_BINDING; 1.
PE 1: Evidence at protein level;
KW ATP-binding; Ligase; Nucleotide-binding; Phenylpropanoid metabolism;
KW Reference proteome.
FT CHAIN 1..554
FT /note="4-coumarate--CoA ligase 3"
FT /id="PRO_0000351624"
FT REGION 261..330
FT /note="SBD1"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT REGION 331..398
FT /note="SBD2"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT BINDING 188..196
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 236
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 331..336
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 335
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 419
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 434
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 525
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
SQ SEQUENCE 554 AA; 59641 MW; 5A1A9D84734BB13C CRC64;
MGSVAAEEVV VFRSKLPDIE IDNSMTLQEY CFARMAEVGA RPCLIDGQTG ESYTYAEVES
ASRRAAAGLR RMGVGKGDVV MSLLRNCPEF AFSFLGAARL GAATTTANPF YTPHEVHRQA
EAAGARVIVT EACAVEKVRE FAAERGVPVV TVDGAFDGCV EFREVLAAEE LDADADVHPD
DVVALPYSSG TTGLPKGVML THRSLITSVA QQVDGENPNL YFSKDDVILC LLPLFHIYSL
NSVLLAGLRA GSTIVIMRKF DLGALVDLVR KHNITIAPFV PPIVVEIAKS PRVTAEDLAS
IRMVMSGAAP MGKDLQDAFM AKIPNAVLGQ GYGMTEAGPV LAMCLAFAKE PFKVKSGSCG
TVVRNAELKI VDPDTGTSLG RNQSGEICIR GEQIMKGYLN DPEATKNTID EDGWLHTGDI
GFVDDDDEIF IVDRLKEIIK YKGFQVPPAE LEALLITHPE IKDAAVVSMK DDLAGEVPVA
FIVRTEGSEI TEDEIKKFVA KEVVFYKRIN KVFFTDSIPK NPSGKILRKD LRARLAAGIP
DAVAAAAADA PKSS
