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Protein

4-coumarate--CoA ligase 1

Gene

4CL1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Produces CoA thioesters of a variety of hydroxy- and methoxy-substituted cinnamic acids, which are used to synthesize several phenylpropanoid-derived compounds, including anthocyanins, flavonoids, isoflavonoids, coumarins, lignin, suberin and wall-bound phenolics.

Catalytic activityi

ATP + 4-coumarate + CoA = AMP + diphosphate + 4-coumaroyl-CoA.1 Publication

Kineticsi

  1. KM=6320 µM for cinnamate
  2. KM=38 µM for 4-coumarate
  3. KM=11 µM for caffeate
  4. KM=199 µM for ferulate

    Pathwayi: 3,4',5-trihydroxystilbene biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes 3,4',5-trihydroxystilbene from trans-4-coumarate.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. 4-coumarate--CoA ligase 1 (4CL1), 4-coumarate--CoA ligase 4 (4CL4), 4-coumarate--CoA ligase 2 (4CL2), 4-coumarate--CoA ligase 3 (4CL3)
    2. no protein annotated in this organism
    This subpathway is part of the pathway 3,4',5-trihydroxystilbene biosynthesis, which is itself part of Phytoalexin biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 3,4',5-trihydroxystilbene from trans-4-coumarate, the pathway 3,4',5-trihydroxystilbene biosynthesis and in Phytoalexin biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei441 – 4411ATPBy similarity
    Binding sitei456 – 4561ATPBy similarity
    Binding sitei547 – 5471ATPBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi210 – 2189ATPBy similarity
    Nucleotide bindingi353 – 3586ATPBy similarity

    GO - Molecular functioni

    • 4-coumarate-CoA ligase activity Source: TAIR
    • ATP binding Source: UniProtKB-KW

    GO - Biological processi

    • phenylpropanoid metabolic process Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Phenylpropanoid metabolism

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciARA:AT1G51680-MONOMER.
    ARA:GQT-1620-MONOMER.
    ARA:GQT-1621-MONOMER.
    MetaCyc:AT1G51680-MONOMER.
    BRENDAi6.2.1.12. 399.
    ReactomeiR-ATH-75105. Fatty Acyl-CoA Biosynthesis.
    SABIO-RKQ42524.
    UniPathwayiUPA00372; UER00547.

    Protein family/group databases

    TCDBi4.C.1.1.7. the proposed fatty acid transporter (fat) family.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-coumarate--CoA ligase 1 (EC:6.2.1.12)
    Short name:
    4CL 1
    Alternative name(s):
    4-coumarate--CoA ligase isoform 1
    Short name:
    At4CL1
    4-coumaroyl-CoA synthase 1
    Gene namesi
    Name:4CL1
    Ordered Locus Names:At1g51680
    ORF Names:F19C24.11
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 1

    Organism-specific databases

    TAIRiAT1G51680.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: TAIR
    Complete GO annotation...

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 5615614-coumarate--CoA ligase 1PRO_0000193027Add
    BLAST

    Proteomic databases

    PaxDbiQ42524.
    PRIDEiQ42524.

    PTM databases

    iPTMnetiQ42524.

    Expressioni

    Tissue specificityi

    Preferentially expressed in roots, bolting stems and siliques. Also detected in leaves.2 Publications

    Inductioni

    By wounding, UV irradiation, and pathogen attack.2 Publications

    Gene expression databases

    ExpressionAtlasiQ42524. baseline and differential.
    GenevisibleiQ42524. AT.

    Interactioni

    Protein-protein interaction databases

    STRINGi3702.AT1G51680.1.

    Structurei

    Secondary structure

    1
    561
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi40 – 445Combined sources
    Turni45 – 473Combined sources
    Helixi48 – 503Combined sources
    Turni51 – 533Combined sources
    Beta strandi54 – 596Combined sources
    Turni60 – 623Combined sources
    Beta strandi65 – 673Combined sources
    Helixi68 – 8417Combined sources
    Beta strandi92 – 965Combined sources
    Helixi101 – 11313Combined sources
    Beta strandi116 – 1205Combined sources
    Helixi126 – 13611Combined sources
    Beta strandi138 – 1436Combined sources
    Turni146 – 1505Combined sources
    Helixi152 – 1565Combined sources
    Beta strandi161 – 1644Combined sources
    Beta strandi177 – 1793Combined sources
    Helixi180 – 1823Combined sources
    Helixi189 – 1935Combined sources
    Beta strandi203 – 2064Combined sources
    Beta strandi213 – 2164Combined sources
    Beta strandi219 – 2235Combined sources
    Helixi224 – 23512Combined sources
    Beta strandi237 – 2393Combined sources
    Beta strandi249 – 2524Combined sources
    Beta strandi256 – 2583Combined sources
    Helixi259 – 2646Combined sources
    Helixi266 – 2727Combined sources
    Beta strandi275 – 2784Combined sources
    Helixi284 – 29411Combined sources
    Beta strandi298 – 3014Combined sources
    Helixi303 – 3119Combined sources
    Helixi313 – 3164Combined sources
    Beta strandi325 – 3306Combined sources
    Helixi337 – 3448Combined sources
    Beta strandi349 – 3524Combined sources
    Helixi357 – 3593Combined sources
    Beta strandi361 – 3655Combined sources
    Helixi367 – 3693Combined sources
    Beta strandi370 – 3723Combined sources
    Beta strandi389 – 3935Combined sources
    Beta strandi407 – 4137Combined sources
    Beta strandi418 – 4203Combined sources
    Helixi424 – 4307Combined sources
    Beta strandi437 – 4459Combined sources
    Beta strandi451 – 4577Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3TSYX-ray3.10A1-561[»]
    ProteinModelPortaliQ42524.
    SMRiQ42524. Positions 22-556.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni283 – 35270SBD11 PublicationAdd
    BLAST
    Regioni353 – 42068SBD21 PublicationAdd
    BLAST

    Domaini

    Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity.1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG1176. Eukaryota.
    COG0318. LUCA.
    HOGENOMiHOG000230009.
    InParanoidiQ42524.
    KOiK01904.
    OMAiKESTDAC.
    PhylomeDBiQ42524.

    Family and domain databases

    InterProiIPR025110. AMP-bd_C.
    IPR020845. AMP-binding_CS.
    IPR000873. AMP-dep_Synth/Lig.
    [Graphical view]
    PfamiPF00501. AMP-binding. 1 hit.
    PF13193. AMP-binding_C. 1 hit.
    [Graphical view]
    PROSITEiPS00455. AMP_BINDING. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q42524-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MAPQEQAVSQ VMEKQSNNNN SDVIFRSKLP DIYIPNHLSL HDYIFQNISE
    60 70 80 90 100
    FATKPCLING PTGHVYTYSD VHVISRQIAA NFHKLGVNQN DVVMLLLPNC
    110 120 130 140 150
    PEFVLSFLAA SFRGATATAA NPFFTPAEIA KQAKASNTKL IITEARYVDK
    160 170 180 190 200
    IKPLQNDDGV VIVCIDDNES VPIPEGCLRF TELTQSTTEA SEVIDSVEIS
    210 220 230 240 250
    PDDVVALPYS SGTTGLPKGV MLTHKGLVTS VAQQVDGENP NLYFHSDDVI
    260 270 280 290 300
    LCVLPMFHIY ALNSIMLCGL RVGAAILIMP KFEINLLLEL IQRCKVTVAP
    310 320 330 340 350
    MVPPIVLAIA KSSETEKYDL SSIRVVKSGA APLGKELEDA VNAKFPNAKL
    360 370 380 390 400
    GQGYGMTEAG PVLAMSLGFA KEPFPVKSGA CGTVVRNAEM KIVDPDTGDS
    410 420 430 440 450
    LSRNQPGEIC IRGHQIMKGY LNNPAATAET IDKDGWLHTG DIGLIDDDDE
    460 470 480 490 500
    LFIVDRLKEL IKYKGFQVAP AELEALLIGH PDITDVAVVA MKEEAAGEVP
    510 520 530 540 550
    VAFVVKSKDS ELSEDDVKQF VSKQVVFYKR INKVFFTESI PKAPSGKILR
    560
    KDLRAKLANG L
    Length:561
    Mass (Da):61,053
    Last modified:November 1, 1996 - v1
    Checksum:i5A9E20816D0C0D07
    GO
    Isoform 2 (identifier: Q42524-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         491-561: Missing.

    Show »
    Length:490
    Mass (Da):53,115
    Checksum:iEA0B03D88A6BC862
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei491 – 56171Missing in isoform 2. 1 PublicationVSP_008911Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18675 mRNA. Translation: AAA82888.1.
    AF106084 Genomic DNA. Translation: AAD47191.1.
    AY376729 mRNA. Translation: AAQ86588.1.
    AC025294 Genomic DNA. Translation: AAG50881.1.
    CP002684 Genomic DNA. Translation: AEE32698.1.
    CP002684 Genomic DNA. Translation: AEE32699.1.
    AY075622 mRNA. Translation: AAL91633.1.
    AY099747 mRNA. Translation: AAM20598.1.
    AY133582 mRNA. Translation: AAM91412.1.
    PIRiS57784.
    RefSeqiNP_175579.1. NM_104046.2. [Q42524-1]
    NP_849793.1. NM_179462.1. [Q42524-2]
    UniGeneiAt.21694.

    Genome annotation databases

    EnsemblPlantsiAT1G51680.1; AT1G51680.1; AT1G51680. [Q42524-1]
    GeneIDi841593.
    KEGGiath:AT1G51680.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U18675 mRNA. Translation: AAA82888.1.
    AF106084 Genomic DNA. Translation: AAD47191.1.
    AY376729 mRNA. Translation: AAQ86588.1.
    AC025294 Genomic DNA. Translation: AAG50881.1.
    CP002684 Genomic DNA. Translation: AEE32698.1.
    CP002684 Genomic DNA. Translation: AEE32699.1.
    AY075622 mRNA. Translation: AAL91633.1.
    AY099747 mRNA. Translation: AAM20598.1.
    AY133582 mRNA. Translation: AAM91412.1.
    PIRiS57784.
    RefSeqiNP_175579.1. NM_104046.2. [Q42524-1]
    NP_849793.1. NM_179462.1. [Q42524-2]
    UniGeneiAt.21694.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3TSYX-ray3.10A1-561[»]
    ProteinModelPortaliQ42524.
    SMRiQ42524. Positions 22-556.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi3702.AT1G51680.1.

    Protein family/group databases

    TCDBi4.C.1.1.7. the proposed fatty acid transporter (fat) family.

    PTM databases

    iPTMnetiQ42524.

    Proteomic databases

    PaxDbiQ42524.
    PRIDEiQ42524.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT1G51680.1; AT1G51680.1; AT1G51680. [Q42524-1]
    GeneIDi841593.
    KEGGiath:AT1G51680.

    Organism-specific databases

    TAIRiAT1G51680.

    Phylogenomic databases

    eggNOGiKOG1176. Eukaryota.
    COG0318. LUCA.
    HOGENOMiHOG000230009.
    InParanoidiQ42524.
    KOiK01904.
    OMAiKESTDAC.
    PhylomeDBiQ42524.

    Enzyme and pathway databases

    UniPathwayiUPA00372; UER00547.
    BioCyciARA:AT1G51680-MONOMER.
    ARA:GQT-1620-MONOMER.
    ARA:GQT-1621-MONOMER.
    MetaCyc:AT1G51680-MONOMER.
    BRENDAi6.2.1.12. 399.
    ReactomeiR-ATH-75105. Fatty Acyl-CoA Biosynthesis.
    SABIO-RKQ42524.

    Miscellaneous databases

    PROiQ42524.

    Gene expression databases

    ExpressionAtlasiQ42524. baseline and differential.
    GenevisibleiQ42524. AT.

    Family and domain databases

    InterProiIPR025110. AMP-bd_C.
    IPR020845. AMP-binding_CS.
    IPR000873. AMP-dep_Synth/Lig.
    [Graphical view]
    PfamiPF00501. AMP-binding. 1 hit.
    PF13193. AMP-binding_C. 1 hit.
    [Graphical view]
    PROSITEiPS00455. AMP_BINDING. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "The Arabidopsis thaliana 4-coumarate:CoA ligase (4CL) gene: stress and developmentally regulated expression and nucleotide sequence of its cDNA."
      Lee D., Ellard M., Wanner L.A., Davis K.R., Douglas C.J.
      Plant Mol. Biol. 28:871-884(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    2. "Three 4-coumarate:coenzyme A ligases in Arabidopsis thaliana represent two evolutionarily divergent classes in angiosperms."
      Ehlting J., Buettner D., Wang Q., Douglas C.J., Somssich I.E., Kombrink E.
      Plant J. 19:9-20(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY, INDUCTION, ENZYME ACTIVITY.
      Strain: cv. Columbia.
    3. "Functional classification of Arabidopsis thaliana 4-coumarate CoA ligase genes."
      Lawrence P.K.
      Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    4. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    5. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    6. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
      Strain: cv. Columbia.
    7. "Identification of 4-coumarate:coenzyme A ligase (4CL) substrate recognition domains."
      Ehlting J., Shin J.J.K., Douglas C.J.
      Plant J. 27:455-465(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBSTRATE-BINDING DOMAINS.
    8. "Arabidopsis contains a large superfamily of acyl-activating enzymes. Phylogenetic and biochemical analysis reveals a new class of acyl-coenzyme a synthetases."
      Shockey J.M., Fulda M.S., Browse J.
      Plant Physiol. 132:1065-1076(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY ORGANIZATION.
    9. "The substrate specificity-determining amino acid code of 4-coumarate:CoA ligase."
      Schneider K., Hoevel K., Witzel K., Hamberger B., Schomburg D., Kombrink E., Stuible H.-P.
      Proc. Natl. Acad. Sci. U.S.A. 100:8601-8606(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: GENE FAMILY ORGANIZATION.
    10. "A new type of peroxisomal acyl-coenzyme A synthetase from Arabidopsis thaliana has the catalytic capacity to activate biosynthetic precursors of jasmonic acid."
      Schneider K., Kienow L., Schmelzer E., Colby T., Bartsch M., Miersch O., Wasternack C., Kombrink E., Stuible H.-P.
      J. Biol. Chem. 280:13962-13972(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: TISSUE SPECIFICITY.
    11. "Multiple cis-regulatory elements regulate distinct and complex patterns of developmental and wound-induced expression of Arabidopsis thaliana 4CL gene family members."
      Soltani B.M., Ehlting J., Hamberger B., Douglas C.J.
      Planta 224:1226-1238(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION BY WOUNDING.

    Entry informationi

    Entry namei4CL1_ARATH
    AccessioniPrimary (citable) accession number: Q42524
    Secondary accession number(s): Q8RY63
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 11, 2001
    Last sequence update: November 1, 1996
    Last modified: June 8, 2016
    This is version 127 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.