4CLL9_ARATH
ID 4CLL9_ARATH Reviewed; 562 AA.
AC Q84P23; Q9FGW4;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 2.
DT 03-AUG-2022, entry version 112.
DE RecName: Full=4-coumarate--CoA ligase-like 9 {ECO:0000303|PubMed:12805634};
DE EC=6.2.1.- {ECO:0000305|PubMed:15677481, ECO:0000305|PubMed:18267944};
DE AltName: Full=4-coumarate--CoA ligase isoform 4;
DE Short=At4CL4;
GN Name=4CLL9 {ECO:0000303|PubMed:12805634};
GN OrderedLocusNames=At5g63380 {ECO:0000312|Araport:AT5G63380};
GN ORFNames=K9H21.11 {ECO:0000312|EMBL:BAB10742.1},
GN K9H21.8 {ECO:0000312|EMBL:BAB10742.1};
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], AND GENE FAMILY ORGANIZATION.
RC STRAIN=cv. Wassilewskija;
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 [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=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
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].
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 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 FUNCTION, SUBCELLULAR LOCATION, ENZYME ACTIVITY, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
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 [9]
RP FUNCTION, DISRUPTION PHENOTYPE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND TISSUE SPECIFICITY.
RX PubMed=18267944; DOI=10.1093/jxb/erm325;
RA Kienow L., Schneider K., Bartsch M., Stuible H.-P., Weng H., Miersch O.,
RA Wasternack C., Kombrink E.;
RT "Jasmonates meet fatty acids: functional analysis of a new acyl-coenzyme A
RT synthetase family from Arabidopsis thaliana.";
RL J. Exp. Bot. 59:403-419(2008).
CC -!- FUNCTION: Contributes to jasmonic acid biosynthesis by initiating the
CC beta-oxidative chain shortening of its precursors (PubMed:15677481,
CC PubMed:18267944). Converts 12-oxo-phytodienoic acid (OPDA) into OPDA-
CC CoA (PubMed:15677481, PubMed:18267944). {ECO:0000269|PubMed:15677481,
CC ECO:0000269|PubMed:18267944}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + hexadecanoate = AMP + diphosphate + hexadecanoyl-
CC CoA; Xref=Rhea:RHEA:30751, ChEBI:CHEBI:7896, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57287, ChEBI:CHEBI:57379,
CC ChEBI:CHEBI:456215; Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:30752;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(9Z)-octadecenoate + ATP + CoA = (9Z)-octadecenoyl-CoA + AMP +
CC diphosphate; Xref=Rhea:RHEA:33607, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:30823, ChEBI:CHEBI:33019, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:57387, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33608;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + octadecanoate = AMP + diphosphate + octadecanoyl-
CC CoA; Xref=Rhea:RHEA:33615, ChEBI:CHEBI:25629, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57287, ChEBI:CHEBI:57394,
CC ChEBI:CHEBI:456215; Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33616;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + tetradecanoate = AMP + diphosphate +
CC tetradecanoyl-CoA; Xref=Rhea:RHEA:33619, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:30807, ChEBI:CHEBI:33019, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:57385, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33620;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + dodecanoate = AMP + diphosphate + dodecanoyl-CoA;
CC Xref=Rhea:RHEA:33623, ChEBI:CHEBI:18262, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57287, ChEBI:CHEBI:57375,
CC ChEBI:CHEBI:456215; Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33624;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + decanoate = AMP + decanoyl-CoA + diphosphate;
CC Xref=Rhea:RHEA:33627, ChEBI:CHEBI:27689, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57287, ChEBI:CHEBI:61430,
CC ChEBI:CHEBI:456215; Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33628;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + octanoate = AMP + diphosphate + octanoyl-CoA;
CC Xref=Rhea:RHEA:33631, ChEBI:CHEBI:25646, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57287, ChEBI:CHEBI:57386,
CC ChEBI:CHEBI:456215; Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33632;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(9Z,12Z)-octadecadienoate + ATP + CoA = (9Z,12Z)-
CC octadecadienoyl-CoA + AMP + diphosphate; Xref=Rhea:RHEA:33651,
CC ChEBI:CHEBI:30245, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57287, ChEBI:CHEBI:57383, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:33652;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(9Z,12Z,15Z)-octadecatrienoate + ATP + CoA = (9Z,12Z,15Z)-
CC octadecatrienoyl-CoA + AMP + diphosphate; Xref=Rhea:RHEA:44936,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:32387, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:57287, ChEBI:CHEBI:74034, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:44937;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(10Z,15Z)-12-oxophytodienoate + ATP + CoA = (10Z,15Z)-12-
CC oxophytodienoyl-CoA + AMP + diphosphate; Xref=Rhea:RHEA:54896,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:57411, ChEBI:CHEBI:138398, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:54897;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + CoA + nonanoate = AMP + diphosphate + nonanoyl-CoA;
CC Xref=Rhea:RHEA:54952, ChEBI:CHEBI:30616, ChEBI:CHEBI:32361,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:57287, ChEBI:CHEBI:76291,
CC ChEBI:CHEBI:456215; Evidence={ECO:0000269|PubMed:18267944};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:54953;
CC Evidence={ECO:0000269|PubMed:18267944};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6302 uM for hexanoic acid {ECO:0000269|PubMed:15677481,
CC ECO:0000269|PubMed:18267944};
CC KM=2125 uM for nonanoic acid {ECO:0000269|PubMed:15677481,
CC ECO:0000269|PubMed:18267944};
CC KM=11 uM for OPDA {ECO:0000269|PubMed:15677481,
CC ECO:0000269|PubMed:18267944};
CC KM=35 uM for hexanoic acid {ECO:0000269|PubMed:15677481,
CC ECO:0000269|PubMed:18267944};
CC Note=kcat is 2 sec(-1) with tetradecanoic acid as substrate
CC (PubMed:15677481, PubMed:18267944). kcat is 2.62 sec(-1) with OPDA as
CC substrate (PubMed:15677481, PubMed:18267944). kcat is 19.87 sec(-1)
CC with nonanoic acid as substrate (PubMed:15677481, PubMed:18267944).
CC kcat is 2.79 sec(-1) with hexanoic acid as substrate
CC (PubMed:15677481, PubMed:18267944). {ECO:0000269|PubMed:15677481,
CC ECO:0000269|PubMed:18267944};
CC -!- SUBCELLULAR LOCATION: Peroxisome {ECO:0000269|PubMed:15677481}.
CC -!- TISSUE SPECIFICITY: Expressed at low level in leaves.
CC {ECO:0000269|PubMed:18267944}.
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 -!- DISRUPTION PHENOTYPE: No obvious phenotype in growth, root and flower
CC development, fertility, reproduction and morphology.
CC {ECO:0000269|PubMed:18267944}.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
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DR EMBL; AY250835; AAP03018.1; -; mRNA.
DR EMBL; AY376731; AAQ86590.1; -; mRNA.
DR EMBL; AB023035; BAB10742.1; -; Genomic_DNA.
DR EMBL; AB007649; BAB10742.1; JOINED; Genomic_DNA.
DR EMBL; CP002688; AED97741.1; -; Genomic_DNA.
DR EMBL; AY136459; AAM97124.1; -; mRNA.
DR EMBL; BT010394; AAQ56837.1; -; mRNA.
DR RefSeq; NP_201143.1; NM_125733.3.
DR AlphaFoldDB; Q84P23; -.
DR SMR; Q84P23; -.
DR STRING; 3702.AT5G63380.1; -.
DR SwissLipids; SLP:000001792; -.
DR iPTMnet; Q84P23; -.
DR PaxDb; Q84P23; -.
DR PRIDE; Q84P23; -.
DR ProteomicsDB; 245107; -.
DR EnsemblPlants; AT5G63380.1; AT5G63380.1; AT5G63380.
DR GeneID; 836457; -.
DR Gramene; AT5G63380.1; AT5G63380.1; AT5G63380.
DR KEGG; ath:AT5G63380; -.
DR Araport; AT5G63380; -.
DR TAIR; locus:2158559; AT5G63380.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q84P23; -.
DR OMA; EYRIICT; -.
DR OrthoDB; 683933at2759; -.
DR PhylomeDB; Q84P23; -.
DR BioCyc; ARA:AT5G63380-MON; -.
DR SABIO-RK; Q84P23; -.
DR PRO; PR:Q84P23; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q84P23; baseline and differential.
DR Genevisible; Q84P23; AT.
DR GO; GO:0005777; C:peroxisome; 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:0102391; F:decanoate-CoA ligase activity; IEA:RHEA.
DR GO; GO:0004321; F:fatty-acyl-CoA synthase activity; IDA:TAIR.
DR GO; GO:0006633; P:fatty acid biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009695; P:jasmonic acid biosynthetic process; IDA:TAIR.
DR GO; GO:0031408; P:oxylipin biosynthetic process; IEA:UniProtKB-KW.
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; Fatty acid biosynthesis; Fatty acid metabolism; Ligase;
KW Lipid biosynthesis; Lipid metabolism; Nucleotide-binding;
KW Oxylipin biosynthesis; Peroxisome; Reference proteome.
FT CHAIN 1..562
FT /note="4-coumarate--CoA ligase-like 9"
FT /id="PRO_0000299182"
FT REGION 283..352
FT /note="SBD1"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT REGION 353..417
FT /note="SBD2"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT MOTIF 560..562
FT /note="Microbody targeting signal"
FT /evidence="ECO:0000255"
FT BINDING 212..216
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 259
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 330..332
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 352..353
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 357
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 438
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 453
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 544
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT CONFLICT 523
FT /note="T -> A (in Ref. 1; AAP03018)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 562 AA; 61278 MW; DE8E87063F2B2DB3 CRC64;
MLTKTNDSRL IDRSSGFDQR TGIYHSLRPS LSLPPIDQPL SAAEFALSLL LKSSPPATAG
KNIEALTYLV NSSSGDNLTY GELLRRVRSL AVSLRERFPS LASRNVAFIL SPSSLDIPVL
YLALMSIGVV VSPANPIGSE SEVSHQVEVS EPVIAFATSQ TVKKLQSSSL PLGTVLMDST
EFLSWLNRSD SSSVNPFQVQ VNQSDPAAIL FSSGTTGRVK GVLLTHRNLI ASTAVSHQRT
LQDPVNYDRV GLFSLPLFHV FGFMMMIRAI SLGETLVLLG RFELEAMFKA VEKYKVTGMP
VSPPLIVALV KSELTKKYDL RSLRSLGCGG APLGKDIAER FKQKFPDVDI VQGYGLTESS
GPAASTFGPE EMVKYGSVGR ISENMEAKIV DPSTGESLPP GKTGELWLRG PVIMKGYVGN
EKASAETVDK EGWLKTGDLC YFDSEDFLYI VDRLKELIKY KAYQVPPVEL EQILHSNPDV
IDAAVVPFPD EDAGEIPMAF IVRKPGSNLN EAQIIDFVAK QVTPYKKVRR VAFINAIPKN
PAGKILRREL TKIAVDGNAS KL
