4CL5_ORYSJ
ID 4CL5_ORYSJ Reviewed; 539 AA.
AC Q6ZAC1; A0A0N7KPY1;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 102.
DE RecName: Full=4-coumarate--CoA ligase 5 {ECO:0000303|PubMed:18627494};
DE Short=4CL 5 {ECO:0000303|PubMed:18627494};
DE Short=Os4CL5 {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 5 {ECO:0000305};
GN Name=4CL5 {ECO:0000303|PubMed:18627494};
GN OrderedLocusNames=Os08g0448000 {ECO:0000312|EMBL:BAT05682.1},
GN LOC_Os08g34790 {ECO:0000305};
GN ORFNames=OsJ_026405 {ECO:0000312|EMBL:EAZ42922.1},
GN P0409A07.17 {ECO:0000312|EMBL:BAD09442.1},
GN P0429B05.38 {ECO:0000312|EMBL:BAD09825.1};
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 [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 [2]
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 [3]
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 [4]
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 [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).
RN [9]
RP INDUCTION BY HEAT STRESS.
RX PubMed=23994682; DOI=10.1016/j.gene.2013.08.048;
RA Zhang X., Rerksiri W., Liu A., Zhou X., Xiong H., Xiang J., Chen X.,
RA Xiong X.;
RT "Transcriptome profile reveals heat response mechanism at molecular and
RT metabolic levels in rice flag leaf.";
RL Gene 530:185-192(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 also able to convert sinapate to its corresponding CoA ester, a
CC reaction that is rarely observed in 4CL catalysis (PubMed:21807887). Is
CC more efficient with substrates in the following order: ferulate > 4-
CC coumarate > sinapate > caffeate > cinnamate (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=54.4 uM for cinnamate {ECO:0000269|PubMed:21807887};
CC KM=10.3 uM for 4-coumarate {ECO:0000269|PubMed:21807887};
CC KM=26.1 uM for caffeate {ECO:0000269|PubMed:21807887};
CC KM=6.9 uM for ferulate {ECO:0000269|PubMed:21807887};
CC KM=58.9 uM for sinapate {ECO:0000269|PubMed:21807887};
CC Vmax=300 pmol/sec/mg enzyme with cinnamate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=830 pmol/sec/mg enzyme with 4-coumarate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=240 pmol/sec/mg enzyme with caffeate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=590 pmol/sec/mg enzyme with ferulate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=920 pmol/sec/mg enzyme with sinapate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Note=kcat is 1.02 min(-1) with cinnamate as substrate
CC (PubMed:21807887). kcat is 2.88 min(-1) with 4-coumarate as substrate
CC (PubMed:21807887). kcat is 0.84 min(-1) with caffeate as substrate
CC (PubMed:21807887). kcat is 2.04 min(-1) with ferulate as substrate
CC (PubMed:21807887). kcat is 3.18 min(-1) with sinapate 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 heat stress (PubMed:23994682). Induced by
CC wounding (PubMed:23246835). Down-regulated by UV irradiation
CC (PubMed:23246835). {ECO:0000269|PubMed:23246835,
CC ECO:0000269|PubMed:23994682}.
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; AP004558; BAD09442.1; -; Genomic_DNA.
DR EMBL; AP004665; BAD09825.1; -; Genomic_DNA.
DR EMBL; AP008214; BAF23849.1; -; Genomic_DNA.
DR EMBL; AP014964; BAT05682.1; -; Genomic_DNA.
DR EMBL; CM000145; EAZ42922.1; -; Genomic_DNA.
DR EMBL; AK120964; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015650830.1; XM_015795344.1.
DR AlphaFoldDB; Q6ZAC1; -.
DR SMR; Q6ZAC1; -.
DR STRING; 4530.OS08T0448000-01; -.
DR PaxDb; Q6ZAC1; -.
DR PRIDE; Q6ZAC1; -.
DR EnsemblPlants; Os08t0448000-01; Os08t0448000-01; Os08g0448000.
DR GeneID; 4345717; -.
DR Gramene; Os08t0448000-01; Os08t0448000-01; Os08g0448000.
DR KEGG; osa:4345717; -.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q6ZAC1; -.
DR OMA; AVWSGDT; -.
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 8.
DR Proteomes; UP000007752; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR Genevisible; Q6ZAC1; 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..539
FT /note="4-coumarate--CoA ligase 5"
FT /id="PRO_0000351626"
FT REGION 258..327
FT /note="SBD1"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT REGION 328..395
FT /note="SBD2"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT BINDING 185..193
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 233
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 328..333
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 332
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 416
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 431
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 522
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT CONFLICT 38
FT /note="D -> G (in Ref. 5; AK120964)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 539 AA; 57045 MW; 08C1BAEF972189FD CRC64;
MGSLPEQFVF RSRLPDIAIP DHLPLHDYVF ERLADRRDRA CLIDGATGET LSFGDVDALS
RRVAAGLSSI GVCHGSTVML LLPNSVEFAV AFLASSRLGA VTTTANPLHT PPEIAKQVAA
SGATVVVTEP AFVAKVSGLA GVTVVATGGG AERCASFAGL AAADGSALPE VAIDVANDAV
ALPYSSGTTG LPKGVMLSHR GLVTSVAQLV DGENPNLHLR EDDVVLCVLP MFHVYSLHSI
LLCGMRAGAA IVVMKRFDTV KMLQLVERHG VTIAPLVPPI VVEMAKSDAL DRHDLSSIRM
VISGAAPMGK ELQDIVHAKL PNAVLGQGYG MTEAGPVLSM CMAFAKEPTP VKSGACGTVV
RNAELKIVDP DTGLSLPRNQ PGEICIRGKQ IMKGYLNNPE ATEKTIDKDG WLHTGDIGFV
DDDDEIFIVD RLKELIKYKG FQVAPAELEA MLIAHAAVAD AAVVPMKDDS CGEIPVAFVV
ARDGSGITDD EIKQYVAKQV VFYKRLHKIF FVDAIPKAPS GKILRKDLRA KLAAGIPAC
