Reviewed, UniProtKB/Swiss-Prot Q42524 (4CL1_ARATH)

Names and origin

Protein names

Recommended name:
    4-coumarate--CoA ligase 1
      Short name=4CL 1
    EC=6.2.1.12
Alternative name(s):
    4-coumarate--CoA ligase isoform 1
      Short name=At4CL1
    4-coumaroyl-CoA synthase 1

Gene names

Name:	4CL1
Ordered Locus Names:	At1g51680
ORF Names:	F19C24.11

Organism

Arabidopsis thaliana (Mouse-ear cress) [Complete proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	561 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	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 activity	ATP + 4-coumarate + CoA = AMP + diphosphate + 4-coumaroyl-CoA. Ref.2
Pathway	Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene biosynthesis; 3,4',5-trihydroxystilbene from 4-coumaric acid: step 1/2.
Tissue specificity	Preferentially expressed in roots, bolting stems and siliques. Also detected in leaves. Ref.2 Ref.9
Induction	By wounding, UV irradiation, and pathogen attack. Ref.2 Ref.10
Domain	Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity. Ref.6
Sequence similarities	Belongs to the ATP-dependent AMP-binding enzyme family.
Biophysicochemical properties	Kinetic parameters: KM=6320 µM for cinnamate KM=38 µM for 4-coumarate KM=11 µM for caffeate KM=199 µM for ferulate

Ontologies

Keywords
Biological process	Phenylpropanoid metabolism
Coding sequence diversity	Alternative splicing
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	phenylpropanoid metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	4-coumarate-CoA ligase activity Ref.2 Inferred from direct assay. Source: TAIR ATP binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q42524-1)

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.

Isoform 2 (identifier: Q42524-2)

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

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 561	561	4-coumarate--CoA ligase 1		PRO_0000193027
Regions
	Nucleotide binding	210 – 218	9	ATP By similarity
	Nucleotide binding	353 – 358	6	ATP By similarity
	Region	283 – 352	70	SBD1
	Region	353 – 420	68	SBD2
Sites
	Binding site	441	1	ATP By similarity
	Binding site	456	1	ATP By similarity
	Binding site	547	1	ATP By similarity
Natural variations
	Alternative sequence	491 – 561	71	Missing in isoform 2.		VSP_008911

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 5A9E20816D0C0D07	FASTA	561	61,053
	10 20 30 40 50 60 MAPQEQAVSQ VMEKQSNNNN SDVIFRSKLP DIYIPNHLSL HDYIFQNISE FATKPCLING 70 80 90 100 110 120 PTGHVYTYSD VHVISRQIAA NFHKLGVNQN DVVMLLLPNC PEFVLSFLAA SFRGATATAA 130 140 150 160 170 180 NPFFTPAEIA KQAKASNTKL IITEARYVDK IKPLQNDDGV VIVCIDDNES VPIPEGCLRF 190 200 210 220 230 240 TELTQSTTEA SEVIDSVEIS PDDVVALPYS SGTTGLPKGV MLTHKGLVTS VAQQVDGENP 250 260 270 280 290 300 NLYFHSDDVI LCVLPMFHIY ALNSIMLCGL RVGAAILIMP KFEINLLLEL IQRCKVTVAP 310 320 330 340 350 360 MVPPIVLAIA KSSETEKYDL SSIRVVKSGA APLGKELEDA VNAKFPNAKL GQGYGMTEAG 370 380 390 400 410 420 PVLAMSLGFA KEPFPVKSGA CGTVVRNAEM KIVDPDTGDS LSRNQPGEIC IRGHQIMKGY 430 440 450 460 470 480 LNNPAATAET IDKDGWLHTG DIGLIDDDDE LFIVDRLKEL IKYKGFQVAP AELEALLIGH 490 500 510 520 530 540 PDITDVAVVA MKEEAAGEVP VAFVVKSKDS ELSEDDVKQF VSKQVVFYKR INKVFFTESI 550 560 PKAPSGKILR KDLRAKLANG L
	Isoform 2. Checksum: EA0B03D88A6BC862	FASTA	490	53,115
	10 20 30 40 50 60 MAPQEQAVSQ VMEKQSNNNN SDVIFRSKLP DIYIPNHLSL HDYIFQNISE FATKPCLING 70 80 90 100 110 120 PTGHVYTYSD VHVISRQIAA NFHKLGVNQN DVVMLLLPNC PEFVLSFLAA SFRGATATAA 130 140 150 160 170 180 NPFFTPAEIA KQAKASNTKL IITEARYVDK IKPLQNDDGV VIVCIDDNES VPIPEGCLRF 190 200 210 220 230 240 TELTQSTTEA SEVIDSVEIS PDDVVALPYS SGTTGLPKGV MLTHKGLVTS VAQQVDGENP 250 260 270 280 290 300 NLYFHSDDVI LCVLPMFHIY ALNSIMLCGL RVGAAILIMP KFEINLLLEL IQRCKVTVAP 310 320 330 340 350 360 MVPPIVLAIA KSSETEKYDL SSIRVVKSGA APLGKELEDA VNAKFPNAKL GQGYGMTEAG 370 380 390 400 410 420 PVLAMSLGFA KEPFPVKSGA CGTVVRNAEM KIVDPDTGDS LSRNQPGEIC IRGHQIMKGY 430 440 450 460 470 480 LNNPAATAET IDKDGWLHTG DIGLIDDDDE LFIVDRLKEL IKYKGFQVAP AELEALLIGH 490 PDITDVAVVA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 7640359] [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: 10417722] [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: 11130712] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[5]	"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: 14593172] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Strain: cv. Columbia.
[6]	"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: 11576429] [Abstract] Cited for: SUBSTRATE-BINDING DOMAINS.
[7]	"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: 12805634] [Abstract] Cited for: GENE FAMILY ORGANIZATION.
[8]	"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: 12819348] [Abstract] Cited for: GENE FAMILY ORGANIZATION.
[9]	"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: 15677481] [Abstract] Cited for: TISSUE SPECIFICITY.
[10]	"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: 16738863] [Abstract] Cited for: INDUCTION BY WOUNDING.

Cross-references

Sequence databases
EMBLGenBankDDBJ	U18675 mRNA. Translation: AAA82888.1. AF106084 Genomic DNA. Translation: AAD47191.1. AY376729 mRNA. Translation: AAQ86588.1. AC025294 Genomic DNA. Translation: AAG50881.1. AY075622 mRNA. Translation: AAL91633.1. AY099747 mRNA. Translation: AAM20598.1. AY133582 mRNA. Translation: AAM91412.1.
IPI	IPI00532346. IPI00547355.
PIR	S57784.
RefSeq	NP_175579.1.
UniGene	At.21694
3D structure databases
HSSP	HSSP built from PDB template 1LCI based on UniProtKB P08659.
ModBase	Search...
Protein family/group databases
TCDB	4.C.1.1.7. proposed fatty acid transporter (FAT) family.
Proteomic databases
PRIDE	Q42524.
Genome annotation databases
GeneID	841593.
GenomeReviews	Gene locus AT1G51680 in contig CT485782_GR.
NMPDR	fig|3702.1.peg.4642.
Organism-specific databases
TAIR	At1g51680.
Phylogenomic databases
OMA	Q42524. ISAMLDI.
Enzyme and pathway databases
BioCyc	MetaCyc:AT1G51680-MON.
BRENDA	6.2.1.12. 302.
Gene expression databases
ArrayExpress	Q42524.
GermOnline	AT1G51680. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR000873. AMP-dep_Synth/Lig. [Graphical view]
Pfam	PF00501. AMP-binding. 1 hit. [Graphical view]
PROSITE	PS00455. AMP_BINDING. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

4CL1_ARATH

Accession

Primary (citable) accession number: Q42524
Secondary accession number(s): Q8RY63

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 11, 2001
Last sequence update:	November 1, 1996
Last modified:	June 16, 2009
This is version 73 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)