Reviewed, UniProtKB/Swiss-Prot Q9S725 (4CL2_ARATH)

Names and origin

Protein names

Recommended name:
    4-coumarate--CoA ligase 2
      Short name=4CL 2
    EC=6.2.1.12
Alternative name(s):
    4-coumarate--CoA ligase isoform 2
      Short name=At4CL2
    4-coumaroyl-CoA synthase 2

Gene names

Name:	4CL2
Ordered Locus Names:	At3g21240
ORF Names:	MXL8.10

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 › malvids › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	556 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.
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 trans-4-coumarate: step 1/2.
Tissue specificity	Preferentially expressed in roots. Ref.1
Induction	By wounding, UV irradiation, and pathogen attack. Ref.1 Ref.11
Domain	Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity. Ref.8
Sequence similarities	Belongs to the ATP-dependent AMP-binding enzyme family.
Biophysicochemical properties	Kinetic parameters: KM=6630 µM for cinnamate KM=252 µM for 4-coumarate KM=20 µM for caffeate

Ontologies

Keywords
Biological process	Phenylpropanoid metabolism
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...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 556	556	4-coumarate--CoA ligase 2		PRO_0000193028
Regions
	Nucleotide binding	203 – 211	9	ATP By similarity
	Nucleotide binding	346 – 351	6	ATP By similarity
	Region	276 – 345	70	SBD1
	Region	346 – 413	68	SBD2
Sites
	Binding site	434	1	ATP By similarity
	Binding site	449	1	ATP By similarity
	Binding site	540	1	ATP By similarity
Experimental info
	Mutagenesis	211	1	K → S: Drastically reduces the activity. Ref.6
	Mutagenesis	293	1	M → A or P: Affects the substrate specificity. Ref.7 Ref.10
	Mutagenesis	320	1	K → L or A: Affects the substrate specificity. Ref.7 Ref.10
	Mutagenesis	401	1	E → Q: Slighlty reduces the substrate specificity. Ref.6
	Mutagenesis	403	1	C → A: Significantly reduces the substrate specificity. Ref.6
	Mutagenesis	449	1	R → Q: Drastically reduces the activity. Ref.6
	Mutagenesis	457	1	K → S: Drastically reduces the activity. Ref.6
	Mutagenesis	540	1	K → N: Abolishes the activity. Ref.6
	Sequence conflict	247	1	L → W in AAD47192. Ref.1
	Sequence conflict	247	1	L → W in AAD47193. Ref.1
	Sequence conflict	265	1	V → I in AAD47192. Ref.1
	Sequence conflict	265	1	V → I in AAD47193. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q9S725-1 [UniParc]. Last modified May 29, 2007. Version 2. Checksum: 26B3305ACB5FAB67	FASTA	556	60,842
	10 20 30 40 50 60 MTTQDVIVND QNDQKQCSND VIFRSRLPDI YIPNHLPLHD YIFENISEFA AKPCLINGPT 70 80 90 100 110 120 GEVYTYADVH VTSRKLAAGL HNLGVKQHDV VMILLPNSPE VVLTFLAASF IGAITTSANP 130 140 150 160 170 180 FFTPAEISKQ AKASAAKLIV TQSRYVDKIK NLQNDGVLIV TTDSDAIPEN CLRFSELTQS 190 200 210 220 230 240 EEPRVDSIPE KISPEDVVAL PFSSGTTGLP KGVMLTHKGL VTSVAQQVDG ENPNLYFNRD 250 260 270 280 290 300 DVILCVLPMF HIYALNSIML CSLRVGATIL IMPKFEITLL LEQIQRCKVT VAMVVPPIVL 310 320 330 340 350 360 AIAKSPETEK YDLSSVRMVK SGAAPLGKEL EDAISAKFPN AKLGQGYGMT EAGPVLAMSL 370 380 390 400 410 420 GFAKEPFPVK SGACGTVVRN AEMKILDPDT GDSLPRNKPG EICIRGNQIM KGYLNDPLAT 430 440 450 460 470 480 ASTIDKDGWL HTGDVGFIDD DDELFIVDRL KELIKYKGFQ VAPAELESLL IGHPEINDVA 490 500 510 520 530 540 VVAMKEEDAG EVPVAFVVRS KDSNISEDEI KQFVSKQVVF YKRINKVFFT DSIPKAPSGK 550 ILRKDLRARL ANGLMN

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]. Strain: cv. Columbia.
[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: 10819329] [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]. Strain: cv. Columbia.
[5]	"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs." Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K. Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 498-556. Strain: cv. Columbia.
[6]	"Mutational analysis of 4-coumarate:CoA ligase identifies functionally important amino acids and verifies its close relationship to other adenylate-forming enzymes." Stuible H.-P., Buettner D., Ehlting J., Hahlbrock K., Kombrink E. FEBS Lett. 467:117-122(2000) [PubMed: 10664468] [Abstract] Cited for: MUTAGENESIS OF LYS-211; GLU-401; CYS-403; ARG-449; LYS-457 AND LYS-540.
[7]	"Identification of the substrate specificity-conferring amino acid residues of 4-coumarate:coenzyme A ligase allows the rational design of mutant enzymes with new catalytic properties." Stuible H.-P., Kombrink E. J. Biol. Chem. 276:26893-26897(2001) [PubMed: 11323416] [Abstract] Cited for: MUTAGENESIS OF MET-293 AND LYS-320.
[8]	"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.
[9]	"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.
[10]	"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, SUBSTRATE RECOGNITION SITES, MUTAGENESIS OF MET-293 AND LYS-320.
[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: 16738863] [Abstract] Cited for: INDUCTION BY WOUNDING.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF106085 Genomic DNA. Translation: AAD47192.1. AF106086 mRNA. Translation: AAD47193.1. AY376728 mRNA. Translation: AAQ86587.1. AB023045 Genomic DNA. Translation: BAB01716.1. AY099695 mRNA. Translation: AAM20546.1. BT000296 mRNA. Translation: AAN15615.1. AK220883 mRNA. Translation: BAD94282.1.
IPI	IPI00526400.
RefSeq	NP_188761.1.
UniGene	At.57587
3D structure databases
SMR	Q9S725. Positions 38-553.
ModBase	Search...
Protein-protein interaction databases
STRING	Q9S725.
Proteomic databases
PRIDE	Q9S725.
Genome annotation databases
GeneID	821678.
GenomeReviews	Gene locus AT3G21240 in contig BA000014_GR.
KEGG	ath:AT3G21240.
NMPDR	fig|3702.1.peg.14358.
Organism-specific databases
TAIR	At3g21240.
Phylogenomic databases
HOGENOM	HBG547964.
InParanoid	Q9S725.
OMA	CFIDAET.
PhylomeDB	Q9S725.
Enzyme and pathway databases
BioCyc	MetaCyc:AT3G21240-MONOMER.
BRENDA	6.2.1.12. 302.
Gene expression databases
ArrayExpress	Q9S725.
Genevestigator	Q9S725.
GermOnline	AT3G21240. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR020845. AMP-binding_CS. 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

4CL2_ARATH

Accession

Primary (citable) accession number: Q9S725
Secondary accession number(s): Q53Z06, Q56ZS8, Q9LU35

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 11, 2001
Last sequence update:	May 29, 2007
Last modified:	February 9, 2010
This is version 70 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)