4CL2_ORYSJ
ID 4CL2_ORYSJ Reviewed; 569 AA.
AC Q42982; B7EY74; Q0DYF5; Q6YUH6;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 27-SEP-2005, sequence version 2.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=4-coumarate--CoA ligase 2 {ECO:0000303|PubMed:18627494};
DE Short=4CL 2 {ECO:0000303|PubMed:18627494};
DE Short=Os4CL2 {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 2 {ECO:0000305};
GN Name=4CL2 {ECO:0000303|PubMed:18627494};
GN Synonyms=4CL.2 {ECO:0000312|EMBL:AAA69580.1};
GN OrderedLocusNames=Os02g0697400 {ECO:0000312|EMBL:BAS80426.1},
GN LOC_Os02g46970 {ECO:0000305};
GN ORFNames=P0459B01.4-1 {ECO:0000312|EMBL:BAD07859.1},
GN P0666E12.12-1 {ECO:0000312|EMBL:BAD08175.1};
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].
RA Zhao Y., Kung S.D., Bottino P.J.;
RT "4-coumarate:CoA ligase genes in rice: divergent structure and differential
RT regulation.";
RL Submitted (JUL-1995) 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 MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
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). Cannot convert
CC sinapate to its corresponding CoA ester (PubMed:21807887,
CC PubMed:23246835). {ECO:0000269|PubMed:21807887,
CC 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=21.7 uM for cinnamate {ECO:0000269|PubMed:21807887};
CC KM=16.8 uM for 4-coumarate {ECO:0000269|PubMed:21807887};
CC KM=21.6 uM for caffeate {ECO:0000269|PubMed:21807887};
CC KM=2.2 uM for ferulate {ECO:0000269|PubMed:21807887};
CC Vmax=299 pmol/sec/mg enzyme with cinnamate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=629 pmol/sec/mg enzyme with 4-coumarate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=708 pmol/sec/mg enzyme with caffeate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=613 pmol/sec/mg enzyme with ferulate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Note=kcat is 1.13 min(-1) with cinnamate as substrate
CC (PubMed:21807887). kcat is 2.37 min(-1) with 4-coumarate as substrate
CC (PubMed:21807887). kcat is 2.67 min(-1) with caffeate as substrate
CC (PubMed:21807887). kcat is 2.31 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 roots, stems, leaf blades, leaf
CC sheaths and spikelets. {ECO:0000269|PubMed:21807887}.
CC -!- INDUCTION: Induced by UV irradiation (PubMed:23246835). Down-regulated
CC by wounding (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 -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
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DR EMBL; L43362; AAA69580.1; -; mRNA.
DR EMBL; AP004778; BAD07859.1; -; Genomic_DNA.
DR EMBL; AP005868; BAD08175.1; -; Genomic_DNA.
DR EMBL; AP008208; BAF09733.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS80426.1; -; Genomic_DNA.
DR EMBL; AK105636; BAG97321.1; -; mRNA.
DR PIR; T03390; T03390.
DR RefSeq; XP_015624111.1; XM_015768625.1.
DR AlphaFoldDB; Q42982; -.
DR SMR; Q42982; -.
DR STRING; 4530.OS02T0697400-01; -.
DR PaxDb; Q42982; -.
DR PRIDE; Q42982; -.
DR EnsemblPlants; Os02t0697400-01; Os02t0697400-01; Os02g0697400.
DR GeneID; 4330407; -.
DR Gramene; Os02t0697400-01; Os02t0697400-01; Os02g0697400.
DR KEGG; osa:4330407; -.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q42982; -.
DR OMA; LGCITHG; -.
DR OrthoDB; 683933at2759; -.
DR BRENDA; 6.2.1.12; 4460.
DR PlantReactome; R-OSA-1119316; Phenylpropanoid biosynthesis.
DR PlantReactome; R-OSA-1119418; Suberin biosynthesis.
DR PlantReactome; R-OSA-1119531; Flavonoid biosynthesis.
DR UniPathway; UPA00372; UER00547.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR Genevisible; Q42982; 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 GO; GO:0010584; P:pollen exine formation; IEA:EnsemblPlants.
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..569
FT /note="4-coumarate--CoA ligase 2"
FT /id="PRO_0000193032"
FT REGION 292..361
FT /note="SBD1"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT REGION 362..429
FT /note="SBD2"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT BINDING 219..227
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 267
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 362..367
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 366
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 450
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 465
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 556
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT CONFLICT 138
FT /note="A -> G (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 186..187
FT /note="EG -> KA (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 226
FT /note="P -> A (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 242..243
FT /note="QQ -> HE (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 277..283
FT /note="CAVRAGA -> SRVRPAP (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 308
FT /note="A -> G (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 316
FT /note="L -> V (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 450
FT /note="D -> N (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
FT CONFLICT 493
FT /note="A -> R (in Ref. 1; AAA69580)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 569 AA; 60815 MW; 2A1A1FF3CF7FEC91 CRC64;
MITVAAPEAQ PQVAAAVDEA PPEAVTVFRS KLPDIDIPSH LPLHEYCFAR AAELPDAPCL
IAAATGRTYT FAETRLLCRR AAAALHRLGV GHGDRVMVLL QNCVEFAVAF FAASFLGAVT
TAANPFCTPQ EIHKQFKASG VKLILTQSVY VDKLRQHEAF PRIDACTVGD DTLTVITIDD
DEATPEGCLP FWDLIADADE GSVPEVAISP DDPVALPFSS GTTGLPKGVV LTHRSVVSGV
AQQVDGENPN LHMGAGDVAL CVLPLFHIFS LNSVLLCAVR AGAAVALMPR FEMGAMLGAI
ERWRVTVAAV VPPLVLALAK NPFVERHDLS SIRIVLSGAA PLGKELEDAL RARLPQAIFG
QGYGMTEAGP VLSMCPAFAK EPTPAKSGSC GTVVRNAELK VVDPDTGFSL GRNLPGEICI
RGPQIMKGYL NDPEATAATI DVEGWLHTGD IGYVDDDDEV FIVDRVKELI KFKGFQVPPA
ELESLLIAHP SIADAAVVPQ KDDVAGEVPV AFVVRAADSD ITEESIKEFI SKQVVFYKRL
HKVHFIHAIP KSASGKILRR ELRAKLAAC
