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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)DescriptionActionsGraphical viewLength
    Binding sitei441ATPBy similarity1
    Binding sitei456ATPBy similarity1
    Binding sitei547ATPBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi210 – 218ATPBy similarity9
    Nucleotide bindingi353 – 358ATPBy similarity6

    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.
    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00001930271 – 5614-coumarate--CoA ligase 1Add BLAST561

    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

    1561
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi40 – 44Combined sources5
    Turni45 – 47Combined sources3
    Helixi48 – 50Combined sources3
    Turni51 – 53Combined sources3
    Beta strandi54 – 59Combined sources6
    Turni60 – 62Combined sources3
    Beta strandi65 – 67Combined sources3
    Helixi68 – 84Combined sources17
    Beta strandi92 – 96Combined sources5
    Helixi101 – 113Combined sources13
    Beta strandi116 – 120Combined sources5
    Helixi126 – 136Combined sources11
    Beta strandi138 – 143Combined sources6
    Turni146 – 150Combined sources5
    Helixi152 – 156Combined sources5
    Beta strandi161 – 164Combined sources4
    Beta strandi177 – 179Combined sources3
    Helixi180 – 182Combined sources3
    Helixi189 – 193Combined sources5
    Beta strandi203 – 206Combined sources4
    Beta strandi213 – 216Combined sources4
    Beta strandi219 – 223Combined sources5
    Helixi224 – 235Combined sources12
    Beta strandi237 – 239Combined sources3
    Beta strandi249 – 252Combined sources4
    Beta strandi256 – 258Combined sources3
    Helixi259 – 264Combined sources6
    Helixi266 – 272Combined sources7
    Beta strandi275 – 278Combined sources4
    Helixi284 – 294Combined sources11
    Beta strandi298 – 301Combined sources4
    Helixi303 – 311Combined sources9
    Helixi313 – 316Combined sources4
    Beta strandi325 – 330Combined sources6
    Helixi337 – 344Combined sources8
    Beta strandi349 – 352Combined sources4
    Helixi357 – 359Combined sources3
    Beta strandi361 – 365Combined sources5
    Helixi367 – 369Combined sources3
    Beta strandi370 – 372Combined sources3
    Beta strandi389 – 393Combined sources5
    Beta strandi407 – 413Combined sources7
    Beta strandi418 – 420Combined sources3
    Helixi424 – 430Combined sources7
    Beta strandi437 – 445Combined sources9
    Beta strandi451 – 457Combined sources7

    3D structure databases

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

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni283 – 352SBD11 PublicationAdd BLAST70
    Regioni353 – 420SBD21 PublicationAdd BLAST68

    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.
    OrthoDBiEOG093606MC.
    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)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_008911491 – 561Missing in isoform 2. 1 PublicationAdd BLAST71

    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_104046.3. [Q42524-1]
    NP_849793.1. NM_179462.2. [Q42524-2]
    UniGeneiAt.21694.

    Genome annotation databases

    EnsemblPlantsiAT1G51680.1; AT1G51680.1; AT1G51680. [Q42524-1]
    GeneIDi841593.
    GrameneiAT1G51680.1; AT1G51680.1; AT1G51680.
    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_104046.3. [Q42524-1]
    NP_849793.1. NM_179462.2. [Q42524-2]
    UniGeneiAt.21694.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3TSYX-ray3.10A1-561[»]
    ProteinModelPortaliQ42524.
    SMRiQ42524.
    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.
    GrameneiAT1G51680.1; AT1G51680.1; AT1G51680.
    KEGGiath:AT1G51680.

    Organism-specific databases

    TAIRiAT1G51680.

    Phylogenomic databases

    eggNOGiKOG1176. Eukaryota.
    COG0318. LUCA.
    HOGENOMiHOG000230009.
    InParanoidiQ42524.
    KOiK01904.
    OMAiKESTDAC.
    OrthoDBiEOG093606MC.
    PhylomeDBiQ42524.

    Enzyme and pathway databases

    UniPathwayiUPA00372; UER00547.
    BioCyciARA:AT1G51680-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...

    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: November 30, 2016
    This is version 131 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.