Reviewed, UniProtKB/Swiss-Prot Q9S777 (4CL3_ARATH)

Names and origin

Protein names

Recommended name:
    4-coumarate--CoA ligase 3
      Short name=4CL 3
    EC=6.2.1.12
Alternative name(s):
    4-coumarate--CoA ligase isoform 3
      Short name=At4CL3
    4-coumaroyl-CoA synthase 3

Gene names

Name:	4CL3
Ordered Locus Names:	At1g65060
ORF Names:	F16G16.6

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.1
Pathway	Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene biosynthesis; 3,4',5-trihydroxystilbene from 4-coumaric acid: step 1/2.
Tissue specificity	Preferentially expressed in leaves, flowers and siliques. Ref.1
Induction	By UV irradiation. Ref.1
Domain	Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity By similarity.
Sequence similarities	Belongs to the ATP-dependent AMP-binding enzyme family.
Biophysicochemical properties	Kinetic parameters: KM=2070 µM for cinnamate KM=23 µM for 4-coumarate KM=374 µM for caffeate KM=166 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 Ref.1 Traceable author statement. Source: TAIR
Molecular function	4-coumarate-CoA ligase activity Ref.1 Inferred from direct assay. Source: TAIR ATP binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 1 isoform produced by alternative splicing. [Select]

Note: A number of isoforms are produced. According to EST sequences.

Isoform 1 (identifier: Q9S777-1)

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.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 561	561	4-coumarate--CoA ligase 3		PRO_0000193029
Regions
	Nucleotide binding	213 – 221	9	ATP By similarity
	Nucleotide binding	356 – 361	6	ATP By similarity
	Region	286 – 355	70	SBD1 By similarity
	Region	356 – 423	68	SBD2 By similarity
Sites
	Binding site	444	1	ATP By similarity
	Binding site	459	1	ATP By similarity
	Binding site	550	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 1, 2000. Version 1. Checksum: C2EFF1C36B33F6DC	FASTA	561	61,311
	10 20 30 40 50 60 MITAALHEPQ IHKPTDTSVV SDDVLPHSPP TPRIFRSKLP DIDIPNHLPL HTYCFEKLSS 70 80 90 100 110 120 VSDKPCLIVG STGKSYTYGE THLICRRVAS GLYKLGIRKG DVIMILLQNS AEFVFSFMGA 130 140 150 160 170 180 SMIGAVSTTA NPFYTSQELY KQLKSSGAKL IITHSQYVDK LKNLGENLTL ITTDEPTPEN 190 200 210 220 230 240 CLPFSTLITD DETNPFQETV DIGGDDAAAL PFSSGTTGLP KGVVLTHKSL ITSVAQQVDG 250 260 270 280 290 300 DNPNLYLKSN DVILCVLPLF HIYSLNSVLL NSLRSGATVL LMHKFEIGAL LDLIQRHRVT 310 320 330 340 350 360 IAALVPPLVI ALAKNPTVNS YDLSSVRFVL SGAAPLGKEL QDSLRRRLPQ AILGQGYGMT 370 380 390 400 410 420 EAGPVLSMSL GFAKEPIPTK SGSCGTVVRN AELKVVHLET RLSLGYNQPG EICIRGQQIM 430 440 450 460 470 480 KEYLNDPEAT SATIDEEGWL HTGDIGYVDE DDEIFIVDRL KEVIKFKGFQ VPPAELESLL 490 500 510 520 530 540 INHHSIADAA VVPQNDEVAG EVPVAFVVRS NGNDITEEDV KEYVAKQVVF YKRLHKVFFV 550 560 ASIPKSPSGK ILRKDLKAKL C

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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 / MRNA], TISSUE SPECIFICITY, INDUCTION, ENZYME ACTIVITY. Strain: cv. Columbia.
[2]	"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].
[3]	"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.
[4]	"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] OF 284-561. Strain: cv. Columbia.
[5]	"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.
[6]	"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.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF106087 Genomic DNA. Translation: AAD47194.1. AF106088 mRNA. Translation: AAD47195.1. AY376730 mRNA. Translation: AAQ86589.1. AC009360 Genomic DNA. Translation: AAF06039.1. AY058083 mRNA. Translation: AAL24191.1. Different initiation. AY090306 mRNA. Translation: AAL90967.1.
IPI	IPI00518931.
PIR	D96674.
RefSeq	NP_176686.1.
UniGene	At.11514
3D structure databases
HSSP	HSSP built from PDB template 1LCI based on UniProtKB P08659.
ModBase	Search...
Proteomic databases
PRIDE	Q9S777.
Genome annotation databases
GeneID	842814.
GenomeReviews	Gene locus AT1G65060 in contig CT485782_GR.
KEGG	ath:AT1G65060.
NMPDR	fig|3702.1.peg.5925.
Organism-specific databases
TAIR	At1g65060.
Phylogenomic databases
OMA	Q9S777. TSATIDE.
Enzyme and pathway databases
BioCyc	MetaCyc:AT1G65060-MON.
BRENDA	6.2.1.12. 302.
Gene expression databases
ArrayExpress	Q9S777.
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

4CL3_ARATH

Accession

Primary (citable) accession number: Q9S777
Secondary accession number(s): Q93Z69

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 11, 2001
Last sequence update:	May 1, 2000
Last modified:	June 16, 2009
This is version 65 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)