Q9LU36 (4CL4_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
4-coumarate--CoA ligase 4
Short name=4CL 4
EC=6.2.1.12

Alternative name(s):
4-coumarate--CoA ligase isoform 5
Short name=At4CL5
4-coumaroyl-CoA synthase 4

Gene names

Name:	4CL4
Ordered Locus Names:	At3g21230
ORF Names:	MXL8_9

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	570 AA.
Sequence status	Complete.
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. Ref.6
Catalytic activity	ATP + 4-coumarate + CoA = AMP + diphosphate + 4-coumaroyl-CoA. Ref.6
Pathway	Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step 1/2.
Induction	By wounding. Ref.8
Domain	Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity By similarity.
Miscellaneous	Activates efficiently sinapate, besides the usual 4CL substrates (4-coumarate, caffeate, and ferulate).
Sequence similarities	Belongs to the ATP-dependent AMP-binding enzyme family.
Biophysicochemical properties	Kinetic parameters: KM=432 µM for 4-coumarate KM=186 µM for caffeate KM=26 µM for ferulate KM=20 µM for sinapate Vmax=100 nmol/sec/mg enzyme with 4-coumarate as substrate Vmax=187 nmol/sec/mg enzyme with caffeate as substrate Vmax=153 nmol/sec/mg enzyme with ferulate as substrate Vmax=105 nmol/sec/mg enzyme with sinapate as substrate
Sequence caution	The sequence AAM19949.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Phenylpropanoid metabolism
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	phenylpropanoid biosynthetic process Inferred from direct assay PubMed 16099486. Source: TAIR
Molecular_function	4-coumarate-CoA ligase activity Inferred from direct assay Ref.6PubMed 16099486. Source: TAIR ATP binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 570	570	4-coumarate--CoA ligase 4		PRO_0000193030
Regions
	Nucleotide binding	218 – 226	9	ATP By similarity
	Nucleotide binding	361 – 366	6	ATP By similarity
	Region	291 – 360	70	SBD1 By similarity
	Region	361 – 427	67	SBD2 By similarity
Sites
	Binding site	448	1	ATP By similarity
	Binding site	463	1	ATP By similarity
	Binding site	554	1	ATP By similarity
Experimental info
	Sequence conflict	81	1	T → I in AAP03020. Ref.1
	Sequence conflict	88	1	A → T in AAP03020. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9LU36 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: 2C2CB71BD5F5860A	FASTA	570	62,559
	10 20 30 40 50 60 MVLQQQTHFL TKKIDQEDEE EEPSHDFIFR SKLPDIFIPN HLPLTDYVFQ RFSGDGDGDS 70 80 90 100 110 120 STTCIIDGAT GRILTYADVQ TNMRRIAAGI HRLGIRHGDV VMLLLPNSPE FALSFLAVAY 130 140 150 160 170 180 LGAVSTTANP FYTQPEIAKQ AKASAAKMII TKKCLVDKLT NLKNDGVLIV CLDDDGDNGV 190 200 210 220 230 240 VSSSDDGCVS FTELTQADET ELLKPKISPE DTVAMPYSSG TTGLPKGVMI THKGLVTSIA 250 260 270 280 290 300 QKVDGENPNL NFTANDVILC FLPMFHIYAL DALMLSAMRT GAALLIVPRF ELNLVMELIQ 310 320 330 340 350 360 RYKVTVVPVA PPVVLAFIKS PETERYDLSS VRIMLSGAAT LKKELEDAVR LKFPNAIFGQ 370 380 390 400 410 420 GYGMTESGTV AKSLAFAKNP FKTKSGACGT VIRNAEMKVV DTETGISLPR NKSGEICVRG 430 440 450 460 470 480 HQLMKGYLND PEATARTIDK DGWLHTGDIG FVDDDDEIFI VDRLKELIKF KGYQVAPAEL 490 500 510 520 530 540 EALLISHPSI DDAAVVAMKD EVADEVPVAF VARSQGSQLT EDDVKSYVNK QVVHYKRIKM 550 560 570 VFFIEVIPKA VSGKILRKDL RAKLETMCSK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: NUCLEOTIDE SEQUENCE [MRNA], GENE FAMILY ORGANIZATION. Strain: cv. Wassilewskija.
[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]	"Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones." Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S. DNA Res. 7:131-135(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[4]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. 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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 26-570. Strain: cv. Columbia.
[6]	"The 4-coumarate:CoA ligase gene family in Arabidopsis thaliana comprises one rare, sinapate-activating and three commonly occurring isoenzymes." Hamberger B., Hahlbrock K. Proc. Natl. Acad. Sci. U.S.A. 101:2209-2214(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ENZYME ACTIVITY.
[7]	"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.
[8]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AY250837 mRNA. Translation: AAP03020.1. AY376732 mRNA. Translation: AAQ86591.1. AB023045 Genomic DNA. Translation: BAB01715.1. CP002686 Genomic DNA. Translation: AEE76479.1. AY095992 mRNA. Translation: AAM19949.1. Different initiation. BT000614 mRNA. Translation: AAN18181.1.
IPI	IPI00521963.
RefSeq	NP_188760.3. NM_113018.3.
UniGene	At.38095.
3D structure databases
ProteinModelPortal	Q9LU36.
SMR	Q9LU36. Positions 26-563.
ModBase	Search...
Proteomic databases
PaxDb	Q9LU36.
PRIDE	Q9LU36.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT3G21230.1; AT3G21230.1; AT3G21230.
GeneID	821677.
KEGG	ath:AT3G21230.
Organism-specific databases
TAIR	At3g21230.
Phylogenomic databases
eggNOG	COG0318.
HOGENOM	HOG000230009.
InParanoid	Q9LU36.
KO	K01904.
OMA	AVYKVPE.
PhylomeDB	Q9LU36.
ProtClustDB	PLN02246.
Enzyme and pathway databases
UniPathway	UPA00372; UER00547.
Gene expression databases
Genevestigator	Q9LU36.
GermOnline	AT3G21230. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR020845. AMP-binding_CS. IPR000873. AMP-dep_Synth/Lig. IPR025110. DUF4009. [Graphical view]
Pfam	PF00501. AMP-binding. 1 hit. PF13193. DUF4009. 1 hit. [Graphical view]
PROSITE	PS00455. AMP_BINDING. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

4CL4_ARATH

Accession

Primary (citable) accession number: Q9LU36
Secondary accession number(s): Q84P22, Q8LPN8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 4, 2005
Last sequence update:	October 1, 2000
Last modified:	May 1, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program