4CL1_ARATH
ID 4CL1_ARATH Reviewed; 561 AA.
AC Q42524; Q8RY63;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=4-coumarate--CoA ligase 1 {ECO:0000303|PubMed:7640359};
DE Short=4CL 1 {ECO:0000303|PubMed:7640359};
DE EC=6.2.1.12 {ECO:0000269|PubMed:10417722};
DE AltName: Full=4-coumarate--CoA ligase isoform 1 {ECO:0000303|PubMed:7640359};
DE Short=At4CL1 {ECO:0000303|PubMed:7640359};
DE AltName: Full=4-coumaroyl-CoA synthase 1 {ECO:0000303|PubMed:7640359};
GN Name=4CL1 {ECO:0000303|PubMed:7640359};
GN OrderedLocusNames=At1g51680 {ECO:0000312|Araport:AT1G51680};
GN ORFNames=F19C24.11 {ECO:0000312|EMBL:AAG50881.1};
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 [MRNA] (ISOFORM 1).
RX PubMed=7640359; DOI=10.1007/bf00042072;
RA Lee D., Ellard M., Wanner L.A., Davis K.R., Douglas C.J.;
RT "The Arabidopsis thaliana 4-coumarate:CoA ligase (4CL) gene: stress and
RT developmentally regulated expression and nucleotide sequence of its cDNA.";
RL Plant Mol. Biol. 28:871-884(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY, INDUCTION, CATALYTIC
RP ACTIVITY, FUNCTION, PATHWAY, AND BIOPHYSICOCHEMICAL PROPERTIES.
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 [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
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 [4]
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 [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
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 [7]
RP SUBSTRATE-BINDING DOMAINS.
RX PubMed=11576429; DOI=10.1046/j.1365-313x.2001.01122.x;
RA Ehlting J., Shin J.J.K., Douglas C.J.;
RT "Identification of 4-coumarate:coenzyme A ligase (4CL) substrate
RT recognition domains.";
RL Plant J. 27:455-465(2001).
RN [8]
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 [9]
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 [10]
RP TISSUE SPECIFICITY.
RX PubMed=15677481; DOI=10.1074/jbc.m413578200;
RA Schneider K., Kienow L., Schmelzer E., Colby T., Bartsch M., Miersch O.,
RA Wasternack C., Kombrink E., Stuible H.-P.;
RT "A new type of peroxisomal acyl-coenzyme A synthetase from Arabidopsis
RT thaliana has the catalytic capacity to activate biosynthetic precursors of
RT jasmonic acid.";
RL J. Biol. Chem. 280:13962-13972(2005).
RN [11]
RP INDUCTION BY WOUNDING.
RX PubMed=16738863; DOI=10.1007/s00425-006-0296-y;
RA Soltani B.M., Ehlting J., Hamberger B., Douglas C.J.;
RT "Multiple cis-regulatory elements regulate distinct and complex patterns of
RT developmental and wound-induced expression of Arabidopsis thaliana 4CL gene
RT family members.";
RL Planta 224:1226-1238(2006).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS).
RX PubMed=22129213; DOI=10.1021/ja2085993;
RA Wang Y., Yi H., Wang M., Yu O., Jez J.M.;
RT "Structural and kinetic analysis of the unnatural fusion protein 4-
RT coumaroyl-CoA ligase::stilbene synthase.";
RL J. Am. Chem. Soc. 133:20684-20687(2011).
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 {ECO:0000269|PubMed:10417722}.
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=6320 uM for cinnamate {ECO:0000269|PubMed:10417722};
CC KM=38 uM for 4-coumarate {ECO:0000269|PubMed:10417722};
CC KM=11 uM for caffeate {ECO:0000269|PubMed:10417722};
CC KM=199 uM for ferulate {ECO:0000269|PubMed:10417722};
CC -!- PATHWAY: Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene
CC biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step
CC 1/2. {ECO:0000269|PubMed:10417722}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q42524-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q42524-2; Sequence=VSP_008911;
CC -!- TISSUE SPECIFICITY: Preferentially expressed in roots, bolting stems
CC and siliques. Also detected in leaves. {ECO:0000269|PubMed:10417722,
CC ECO:0000269|PubMed:15677481}.
CC -!- INDUCTION: By wounding, UV irradiation, and pathogen attack.
CC {ECO:0000269|PubMed:10417722, ECO:0000269|PubMed:16738863}.
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:0000269|PubMed:11576429}.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
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DR EMBL; U18675; AAA82888.1; -; mRNA.
DR EMBL; AF106084; AAD47191.1; -; Genomic_DNA.
DR EMBL; AY376729; AAQ86588.1; -; mRNA.
DR EMBL; AC025294; AAG50881.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32698.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE32699.1; -; Genomic_DNA.
DR EMBL; AY075622; AAL91633.1; -; mRNA.
DR EMBL; AY099747; AAM20598.1; -; mRNA.
DR EMBL; AY133582; AAM91412.1; -; mRNA.
DR PIR; S57784; S57784.
DR RefSeq; NP_175579.1; NM_104046.3. [Q42524-1]
DR RefSeq; NP_849793.1; NM_179462.2. [Q42524-2]
DR PDB; 3TSY; X-ray; 3.10 A; A=1-561.
DR PDBsum; 3TSY; -.
DR AlphaFoldDB; Q42524; -.
DR SMR; Q42524; -.
DR STRING; 3702.AT1G51680.1; -.
DR TCDB; 4.C.1.1.7; the fatty acid group translocation (fat) family.
DR iPTMnet; Q42524; -.
DR MetOSite; Q42524; -.
DR PaxDb; Q42524; -.
DR PRIDE; Q42524; -.
DR ProteomicsDB; 245088; -. [Q42524-1]
DR EnsemblPlants; AT1G51680.1; AT1G51680.1; AT1G51680. [Q42524-1]
DR EnsemblPlants; AT1G51680.2; AT1G51680.2; AT1G51680. [Q42524-2]
DR GeneID; 841593; -.
DR Gramene; AT1G51680.1; AT1G51680.1; AT1G51680. [Q42524-1]
DR Gramene; AT1G51680.2; AT1G51680.2; AT1G51680. [Q42524-2]
DR KEGG; ath:AT1G51680; -.
DR Araport; AT1G51680; -.
DR TAIR; locus:2017602; AT1G51680.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q42524; -.
DR OMA; DFGGWKI; -.
DR PhylomeDB; Q42524; -.
DR BioCyc; ARA:AT1G51680-MON; -.
DR BioCyc; MetaCyc:AT1G51680-MON; -.
DR BRENDA; 6.2.1.12; 399.
DR SABIO-RK; Q42524; -.
DR UniPathway; UPA00372; UER00547.
DR PRO; PR:Q42524; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q42524; baseline and differential.
DR Genevisible; Q42524; AT.
DR GO; GO:0005737; C:cytoplasm; IDA:TAIR.
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:0009698; P:phenylpropanoid metabolic process; TAS: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 3D-structure; Alternative splicing; ATP-binding; Ligase;
KW Nucleotide-binding; Phenylpropanoid metabolism; Reference proteome.
FT CHAIN 1..561
FT /note="4-coumarate--CoA ligase 1"
FT /id="PRO_0000193027"
FT REGION 283..352
FT /note="SBD1"
FT /evidence="ECO:0000269|PubMed:11576429"
FT REGION 353..420
FT /note="SBD2"
FT /evidence="ECO:0000269|PubMed:11576429"
FT BINDING 210..218
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q81G39"
FT BINDING 352..357
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q81G39"
FT BINDING 441
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q81G39"
FT BINDING 453..456
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q81G39"
FT BINDING 547
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q81G39"
FT VAR_SEQ 491..561
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_008911"
FT HELIX 40..44
FT /evidence="ECO:0007829|PDB:3TSY"
FT TURN 45..47
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:3TSY"
FT TURN 51..53
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 54..59
FT /evidence="ECO:0007829|PDB:3TSY"
FT TURN 60..62
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 68..84
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 92..96
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 101..113
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 116..120
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 126..136
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 138..143
FT /evidence="ECO:0007829|PDB:3TSY"
FT TURN 146..150
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 152..156
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 177..179
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 189..193
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 203..206
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 219..223
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 224..235
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 256..258
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 259..264
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 266..272
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 275..278
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 284..294
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 298..301
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 303..311
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 313..316
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 325..330
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 337..344
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 349..352
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 357..359
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 361..365
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 367..369
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 370..372
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 389..393
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 407..413
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 418..420
FT /evidence="ECO:0007829|PDB:3TSY"
FT HELIX 424..430
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 437..445
FT /evidence="ECO:0007829|PDB:3TSY"
FT STRAND 451..457
FT /evidence="ECO:0007829|PDB:3TSY"
SQ SEQUENCE 561 AA; 61053 MW; 5A9E20816D0C0D07 CRC64;
MAPQEQAVSQ VMEKQSNNNN SDVIFRSKLP DIYIPNHLSL HDYIFQNISE FATKPCLING
PTGHVYTYSD VHVISRQIAA NFHKLGVNQN DVVMLLLPNC PEFVLSFLAA SFRGATATAA
NPFFTPAEIA KQAKASNTKL IITEARYVDK IKPLQNDDGV VIVCIDDNES VPIPEGCLRF
TELTQSTTEA SEVIDSVEIS PDDVVALPYS SGTTGLPKGV MLTHKGLVTS VAQQVDGENP
NLYFHSDDVI LCVLPMFHIY ALNSIMLCGL RVGAAILIMP KFEINLLLEL IQRCKVTVAP
MVPPIVLAIA KSSETEKYDL SSIRVVKSGA APLGKELEDA VNAKFPNAKL GQGYGMTEAG
PVLAMSLGFA KEPFPVKSGA CGTVVRNAEM KIVDPDTGDS LSRNQPGEIC IRGHQIMKGY
LNNPAATAET IDKDGWLHTG DIGLIDDDDE LFIVDRLKEL IKYKGFQVAP AELEALLIGH
PDITDVAVVA MKEEAAGEVP VAFVVKSKDS ELSEDDVKQF VSKQVVFYKR INKVFFTESI
PKAPSGKILR KDLRAKLANG L
