4CL2_ARATH
ID 4CL2_ARATH Reviewed; 556 AA.
AC Q9S725; Q53Z06; Q56ZS8; Q9LU35;
DT 11-JAN-2001, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2007, sequence version 2.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=4-coumarate--CoA ligase 2;
DE Short=4CL 2;
DE EC=6.2.1.12;
DE AltName: Full=4-coumarate--CoA ligase isoform 2;
DE Short=At4CL2;
DE AltName: Full=4-coumaroyl-CoA synthase 2;
GN Name=4CL2; OrderedLocusNames=At3g21240; ORFNames=MXL8.10;
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].
RC STRAIN=cv. Columbia;
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=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(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].
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 498-556.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP MUTAGENESIS OF LYS-211; GLU-401; CYS-403; ARG-449; LYS-457 AND LYS-540.
RX PubMed=10664468; DOI=10.1016/s0014-5793(00)01133-9;
RA Stuible H.-P., Buettner D., Ehlting J., Hahlbrock K., Kombrink E.;
RT "Mutational analysis of 4-coumarate:CoA ligase identifies functionally
RT important amino acids and verifies its close relationship to other
RT adenylate-forming enzymes.";
RL FEBS Lett. 467:117-122(2000).
RN [8]
RP MUTAGENESIS OF MET-293 AND LYS-320.
RX PubMed=11323416; DOI=10.1074/jbc.m100355200;
RA Stuible H.-P., Kombrink E.;
RT "Identification of the substrate specificity-conferring amino acid residues
RT of 4-coumarate:coenzyme A ligase allows the rational design of mutant
RT enzymes with new catalytic properties.";
RL J. Biol. Chem. 276:26893-26897(2001).
RN [9]
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 [10]
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 [11]
RP GENE FAMILY ORGANIZATION, SUBSTRATE RECOGNITION SITES, AND MUTAGENESIS OF
RP MET-293 AND LYS-320.
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 [12]
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 [13]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT THR-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
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=6630 uM for cinnamate;
CC KM=252 uM for 4-coumarate;
CC KM=20 uM for caffeate;
CC -!- PATHWAY: Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene
CC biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step
CC 1/2.
CC -!- TISSUE SPECIFICITY: Preferentially expressed in roots.
CC {ECO:0000269|PubMed:10417722}.
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.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
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DR EMBL; AF106085; AAD47192.1; -; Genomic_DNA.
DR EMBL; AF106086; AAD47193.1; -; mRNA.
DR EMBL; AY376728; AAQ86587.1; -; mRNA.
DR EMBL; AB023045; BAB01716.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE76480.1; -; Genomic_DNA.
DR EMBL; AY099695; AAM20546.1; -; mRNA.
DR EMBL; BT000296; AAN15615.1; -; mRNA.
DR EMBL; AK220883; BAD94282.1; -; mRNA.
DR RefSeq; NP_188761.1; NM_113019.4.
DR AlphaFoldDB; Q9S725; -.
DR SMR; Q9S725; -.
DR STRING; 3702.AT3G21240.1; -.
DR iPTMnet; Q9S725; -.
DR PaxDb; Q9S725; -.
DR PRIDE; Q9S725; -.
DR ProteomicsDB; 245136; -.
DR EnsemblPlants; AT3G21240.1; AT3G21240.1; AT3G21240.
DR GeneID; 821678; -.
DR Gramene; AT3G21240.1; AT3G21240.1; AT3G21240.
DR KEGG; ath:AT3G21240; -.
DR Araport; AT3G21240; -.
DR TAIR; locus:2094716; AT3G21240.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q9S725; -.
DR OMA; WFLIANY; -.
DR OrthoDB; 683933at2759; -.
DR PhylomeDB; Q9S725; -.
DR BioCyc; ARA:AT3G21240-MON; -.
DR BioCyc; MetaCyc:AT3G21240-MON; -.
DR BRENDA; 6.2.1.12; 399.
DR SABIO-RK; Q9S725; -.
DR UniPathway; UPA00372; UER00547.
DR PRO; PR:Q9S725; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9S725; baseline and differential.
DR Genevisible; Q9S725; 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: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 Acetylation; ATP-binding; Ligase; Nucleotide-binding;
KW Phenylpropanoid metabolism; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..556
FT /note="4-coumarate--CoA ligase 2"
FT /id="PRO_0000193028"
FT REGION 276..345
FT /note="SBD1"
FT REGION 346..413
FT /note="SBD2"
FT BINDING 203..211
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 346..351
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 434
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 449
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 540
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 2
FT /note="N-acetylthreonine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MUTAGEN 211
FT /note="K->S: Drastically reduces the activity."
FT /evidence="ECO:0000269|PubMed:10664468"
FT MUTAGEN 293
FT /note="M->A,P: Affects the substrate specificity."
FT /evidence="ECO:0000269|PubMed:11323416,
FT ECO:0000269|PubMed:12819348"
FT MUTAGEN 320
FT /note="K->L,A: Affects the substrate specificity."
FT /evidence="ECO:0000269|PubMed:11323416,
FT ECO:0000269|PubMed:12819348"
FT MUTAGEN 401
FT /note="E->Q: Slighlty reduces the substrate specificity."
FT /evidence="ECO:0000269|PubMed:10664468"
FT MUTAGEN 403
FT /note="C->A: Significantly reduces the substrate
FT specificity."
FT /evidence="ECO:0000269|PubMed:10664468"
FT MUTAGEN 449
FT /note="R->Q: Drastically reduces the activity."
FT /evidence="ECO:0000269|PubMed:10664468"
FT MUTAGEN 457
FT /note="K->S: Drastically reduces the activity."
FT /evidence="ECO:0000269|PubMed:10664468"
FT MUTAGEN 540
FT /note="K->N: Abolishes the activity."
FT /evidence="ECO:0000269|PubMed:10664468"
FT CONFLICT 247
FT /note="L -> W (in Ref. 1; AAD47192/AAD47193)"
FT /evidence="ECO:0000305"
FT CONFLICT 265
FT /note="V -> I (in Ref. 1; AAD47192/AAD47193)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 556 AA; 60842 MW; 26B3305ACB5FAB67 CRC64;
MTTQDVIVND QNDQKQCSND VIFRSRLPDI YIPNHLPLHD YIFENISEFA AKPCLINGPT
GEVYTYADVH VTSRKLAAGL HNLGVKQHDV VMILLPNSPE VVLTFLAASF IGAITTSANP
FFTPAEISKQ AKASAAKLIV TQSRYVDKIK NLQNDGVLIV TTDSDAIPEN CLRFSELTQS
EEPRVDSIPE KISPEDVVAL PFSSGTTGLP KGVMLTHKGL VTSVAQQVDG ENPNLYFNRD
DVILCVLPMF HIYALNSIML CSLRVGATIL IMPKFEITLL LEQIQRCKVT VAMVVPPIVL
AIAKSPETEK YDLSSVRMVK SGAAPLGKEL EDAISAKFPN AKLGQGYGMT EAGPVLAMSL
GFAKEPFPVK SGACGTVVRN AEMKILDPDT GDSLPRNKPG EICIRGNQIM KGYLNDPLAT
ASTIDKDGWL HTGDVGFIDD DDELFIVDRL KELIKYKGFQ VAPAELESLL IGHPEINDVA
VVAMKEEDAG EVPVAFVVRS KDSNISEDEI KQFVSKQVVF YKRINKVFFT DSIPKAPSGK
ILRKDLRARL ANGLMN
