4CL3_ARATH
ID 4CL3_ARATH Reviewed; 561 AA.
AC Q9S777; Q93Z69;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=4-coumarate--CoA ligase 3;
DE Short=4CL 3;
DE EC=6.2.1.12;
DE AltName: Full=4-coumarate--CoA ligase isoform 3;
DE Short=At4CL3;
DE AltName: Full=4-coumaroyl-CoA synthase 3;
GN Name=4CL3; OrderedLocusNames=At1g65060; ORFNames=F16G16.6;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], TISSUE SPECIFICITY, INDUCTION,
RP AND ENZYME ACTIVITY.
RC STRAIN=cv. Columbia;
RX PubMed=10417722; DOI=10.1046/j.1365-313x.1999.00491.x;
RA Ehlting J., Buettner D., Wang Q., Douglas C.J., Somssich I.E., Kombrink E.;
RT "Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two
RT evolutionarily divergent classes in angiosperms.";
RL Plant J. 19:9-20(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Lawrence P.K.;
RT "Functional classification of Arabidopsis thaliana 4-coumarate CoA ligase
RT genes.";
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 284-561.
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP GENE FAMILY ORGANIZATION.
RX PubMed=12805634; DOI=10.1104/pp.103.020552;
RA Shockey J.M., Fulda M.S., Browse J.;
RT "Arabidopsis contains a large superfamily of acyl-activating enzymes.
RT Phylogenetic and biochemical analysis reveals a new class of acyl-coenzyme
RT a synthetases.";
RL Plant Physiol. 132:1065-1076(2003).
RN [7]
RP GENE FAMILY ORGANIZATION.
RX PubMed=12819348; DOI=10.1073/pnas.1430550100;
RA Schneider K., Hoevel K., Witzel K., Hamberger B., Schomburg D.,
RA Kombrink E., Stuible H.-P.;
RT "The substrate specificity-determining amino acid code of 4-coumarate:CoA
RT ligase.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:8601-8606(2003).
RN [8]
RP REVIEW, AND NOMENCLATURE.
RX PubMed=23473981; DOI=10.1016/j.plaphy.2013.02.001;
RA Saito K., Yonekura-Sakakibara K., Nakabayashi R., Higashi Y., Yamazaki M.,
RA Tohge T., Fernie A.R.;
RT "The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic
RT diversity.";
RL Plant Physiol. Biochem. 72:21-34(2013).
CC -!- FUNCTION: Produces CoA thioesters of a variety of hydroxy- and methoxy-
CC substituted cinnamic acids, which are used to synthesize several
CC phenylpropanoid-derived compounds, including anthocyanins, flavonoids,
CC isoflavonoids, coumarins, lignin, suberin and wall-bound phenolics.
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:10417722};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2070 uM for cinnamate;
CC KM=23 uM for 4-coumarate;
CC KM=374 uM for caffeate;
CC KM=166 uM for ferulate;
CC -!- PATHWAY: Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene
CC biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step
CC 1/2.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=1;
CC Comment=A number of isoforms are produced. According to EST
CC sequences.;
CC Name=1;
CC IsoId=Q9S777-1; Sequence=Displayed;
CC -!- TISSUE SPECIFICITY: Preferentially expressed in leaves, flowers and
CC siliques. {ECO:0000269|PubMed:10417722}.
CC -!- INDUCTION: By UV irradiation. {ECO:0000269|PubMed:10417722}.
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}.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAL24191.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AF106087; AAD47194.1; -; Genomic_DNA.
DR EMBL; AF106088; AAD47195.1; -; mRNA.
DR EMBL; AY376730; AAQ86589.1; -; mRNA.
DR EMBL; AC009360; AAF06039.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE34323.1; -; Genomic_DNA.
DR EMBL; AY058083; AAL24191.1; ALT_INIT; mRNA.
DR EMBL; AY090306; AAL90967.1; -; mRNA.
DR PIR; D96674; D96674.
DR RefSeq; NP_176686.1; NM_105180.4. [Q9S777-1]
DR AlphaFoldDB; Q9S777; -.
DR SMR; Q9S777; -.
DR STRING; 3702.AT1G65060.1; -.
DR PaxDb; Q9S777; -.
DR PRIDE; Q9S777; -.
DR ProteomicsDB; 244548; -. [Q9S777-1]
DR EnsemblPlants; AT1G65060.1; AT1G65060.1; AT1G65060. [Q9S777-1]
DR GeneID; 842814; -.
DR Gramene; AT1G65060.1; AT1G65060.1; AT1G65060. [Q9S777-1]
DR KEGG; ath:AT1G65060; -.
DR Araport; AT1G65060; -.
DR TAIR; locus:2015003; AT1G65060.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q9S777; -.
DR OMA; LGCITHG; -.
DR OrthoDB; 683933at2759; -.
DR PhylomeDB; Q9S777; -.
DR BioCyc; ARA:AT1G65060-MON; -.
DR BioCyc; MetaCyc:AT1G65060-MON; -.
DR BRENDA; 6.2.1.12; 399.
DR SABIO-RK; Q9S777; -.
DR UniPathway; UPA00372; UER00547.
DR PRO; PR:Q9S777; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9S777; baseline and differential.
DR Genevisible; Q9S777; AT.
DR GO; GO:0016207; F:4-coumarate-CoA ligase activity; IDA:TAIR.
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; IEA:EnsemblPlants.
DR GO; GO:0009698; P:phenylpropanoid metabolic process; TAS:TAIR.
DR GO; GO:0010584; P:pollen exine formation; IMP:TAIR.
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 Alternative splicing; ATP-binding; Ligase; Nucleotide-binding;
KW Phenylpropanoid metabolism; Reference proteome.
FT CHAIN 1..561
FT /note="4-coumarate--CoA ligase 3"
FT /id="PRO_0000193029"
FT REGION 286..355
FT /note="SBD1"
FT /evidence="ECO:0000250"
FT REGION 356..423
FT /note="SBD2"
FT /evidence="ECO:0000250"
FT BINDING 213..221
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 356..361
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 444
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 459
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 550
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
SQ SEQUENCE 561 AA; 61311 MW; C2EFF1C36B33F6DC CRC64;
MITAALHEPQ IHKPTDTSVV SDDVLPHSPP TPRIFRSKLP DIDIPNHLPL HTYCFEKLSS
VSDKPCLIVG STGKSYTYGE THLICRRVAS GLYKLGIRKG DVIMILLQNS AEFVFSFMGA
SMIGAVSTTA NPFYTSQELY KQLKSSGAKL IITHSQYVDK LKNLGENLTL ITTDEPTPEN
CLPFSTLITD DETNPFQETV DIGGDDAAAL PFSSGTTGLP KGVVLTHKSL ITSVAQQVDG
DNPNLYLKSN DVILCVLPLF HIYSLNSVLL NSLRSGATVL LMHKFEIGAL LDLIQRHRVT
IAALVPPLVI ALAKNPTVNS YDLSSVRFVL SGAAPLGKEL QDSLRRRLPQ AILGQGYGMT
EAGPVLSMSL GFAKEPIPTK SGSCGTVVRN AELKVVHLET RLSLGYNQPG EICIRGQQIM
KEYLNDPEAT SATIDEEGWL HTGDIGYVDE DDEIFIVDRL KEVIKFKGFQ VPPAELESLL
INHHSIADAA VVPQNDEVAG EVPVAFVVRS NGNDITEEDV KEYVAKQVVF YKRLHKVFFV
ASIPKSPSGK ILRKDLKAKL C
