4CL4_ORYSJ
ID 4CL4_ORYSJ Reviewed; 559 AA.
AC Q67W82; B7EFQ0; Q67W81;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2004, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=4-coumarate--CoA ligase 4 {ECO:0000303|PubMed:18627494};
DE Short=4CL 4 {ECO:0000303|PubMed:18627494};
DE Short=Os4CL4 {ECO:0000303|PubMed:18627494};
DE EC=6.2.1.12 {ECO:0000269|PubMed:21807887, ECO:0000269|PubMed:23246835};
DE AltName: Full=4-coumaroyl-CoA synthase 4 {ECO:0000305};
DE AltName: Full=Protein RESISTANCE TO ALUMINUM 1 {ECO:0000303|PubMed:32989851};
GN Name=4CL4 {ECO:0000303|PubMed:18627494};
GN Synonyms=RAL1 {ECO:0000303|PubMed:32989851};
GN OrderedLocusNames=Os06g0656500 {ECO:0000312|EMBL:BAS98942.1},
GN LOC_Os06g44620 {ECO:0000305};
GN ORFNames=P0460H04.31-1 {ECO:0000312|EMBL:BAD37587.1},
GN P0460H04.31-2 {ECO:0000312|EMBL:BAD37588.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [5]
RP GENE FAMILY.
RX PubMed=18627494; DOI=10.1111/j.1469-8137.2008.02534.x;
RA de Azevedo Souza C., Barbazuk B., Ralph S.G., Bohlmann J., Hamberger B.,
RA Douglas C.J.;
RT "Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase
RT (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella.";
RL New Phytol. 179:987-1003(2008).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND TISSUE
RP SPECIFICITY.
RX PubMed=21807887; DOI=10.1104/pp.111.178301;
RA Gui J., Shen J., Li L.;
RT "Functional characterization of evolutionarily divergent 4-
RT coumarate:coenzyme a ligases in rice.";
RL Plant Physiol. 157:574-586(2011).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND INDUCTION.
RX PubMed=23246835; DOI=10.1016/j.bbrc.2012.12.019;
RA Sun H., Li Y., Feng S., Zou W., Guo K., Fan C., Si S., Peng L.;
RT "Analysis of five rice 4-coumarate:coenzyme A ligase enzyme activity and
RT stress response for potential roles in lignin and flavonoid biosynthesis in
RT rice.";
RL Biochem. Biophys. Res. Commun. 430:1151-1156(2013).
RN [8]
RP INDUCTION BY HEAT STRESS.
RX PubMed=23994682; DOI=10.1016/j.gene.2013.08.048;
RA Zhang X., Rerksiri W., Liu A., Zhou X., Xiong H., Xiang J., Chen X.,
RA Xiong X.;
RT "Transcriptome profile reveals heat response mechanism at molecular and
RT metabolic levels in rice flag leaf.";
RL Gene 530:185-192(2013).
RN [9]
RP FUNCTION, SUBCELLULAR LOCATION, INDUCTION, AND MUTAGENESIS OF GLY-395.
RX PubMed=32989851; DOI=10.1111/tpj.14995;
RA Liu S., Zhao L., Liao Y., Luo Z., Wang H., Wang P., Zhao H., Xia J.,
RA Huang C.F.;
RT "Dysfunction of the 4-coumarate:coenzyme A ligase 4CL4 impacts aluminum
RT resistance and lignin accumulation in rice.";
RL Plant J. 104:1233-1250(2020).
CC -!- FUNCTION: Involved in the phenylpropanoid metabolism by mediating the
CC activation of a number of hydroxycinnamates for the biosynthesis of
CC monolignols and other phenolic secondary metabolites (PubMed:21807887,
CC PubMed:23246835). Catalyzes the formation of CoA esters of cinnamate,
CC 4-coumarate, caffeate and ferulate (PubMed:21807887, PubMed:23246835).
CC Is more efficient with substrates in the following order: 4-coumarate >
CC ferulate > caffeate > cinnamate (PubMed:21807887). Cannot convert
CC sinapate to its corresponding CoA ester (PubMed:21807887,
CC PubMed:23246835). Required for the biosynthesis of lignin in roots and
CC shoots (PubMed:32989851). {ECO:0000269|PubMed:21807887,
CC ECO:0000269|PubMed:23246835, ECO:0000269|PubMed:32989851}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(E)-4-coumarate + ATP + CoA = (E)-4-coumaroyl-CoA + AMP +
CC diphosphate; Xref=Rhea:RHEA:19641, ChEBI:CHEBI:12876,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:85008, ChEBI:CHEBI:456215; EC=6.2.1.12;
CC Evidence={ECO:0000269|PubMed:21807887, ECO:0000269|PubMed:23246835};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:19642;
CC Evidence={ECO:0000269|PubMed:21807887, ECO:0000269|PubMed:23246835};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15.7 uM for cinnamate {ECO:0000269|PubMed:21807887};
CC KM=3.9 uM for 4-coumarate {ECO:0000269|PubMed:21807887};
CC KM=5.8 uM for caffeate {ECO:0000269|PubMed:21807887};
CC KM=4.6 uM for ferulate {ECO:0000269|PubMed:21807887};
CC Vmax=350 pmol/sec/mg enzyme with cinnamate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=770 pmol/sec/mg enzyme with 4-coumarate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=590 pmol/sec/mg enzyme with caffeate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Vmax=520 pmol/sec/mg enzyme with ferulate as substrate
CC {ECO:0000269|PubMed:21807887};
CC Note=kcat is 1.28 min(-1) with cinnamate as substrate
CC (PubMed:21807887). kcat is 2.82 min(-1) with 4-coumarate as substrate
CC (PubMed:21807887). kcat is 2.16 min(-1) with caffeate as substrate
CC (PubMed:21807887). kcat is 1.92 min(-1) with ferulate as substrate
CC (PubMed:21807887). {ECO:0000269|PubMed:21807887};
CC -!- PATHWAY: Phytoalexin biosynthesis; 3,4',5-trihydroxystilbene
CC biosynthesis; 3,4',5-trihydroxystilbene from trans-4-coumarate: step
CC 1/2. {ECO:0000305}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:32989851}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q67W82-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q67W82-2; Sequence=VSP_035525, VSP_035526;
CC -!- TISSUE SPECIFICITY: Expressed in roots, stems, leaf blades and leaf
CC sheaths. {ECO:0000269|PubMed:21807887}.
CC -!- INDUCTION: Induced by heat stress (PubMed:23994682). Induced by
CC wounding (PubMed:23246835). Down-regulated by UV irradiation
CC (PubMed:23246835, PubMed:23994682). Down-regulated by aluminum stress
CC (PubMed:32989851). {ECO:0000269|PubMed:23246835,
CC ECO:0000269|PubMed:23994682, ECO:0000269|PubMed:32989851}.
CC -!- DOMAIN: Both substrate-binding domains (SBD1 and SBD2) are involved in
CC the substrate recognition, and are sufficient to confer the substrate
CC specificity. {ECO:0000250|UniProtKB:Q42524}.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC {ECO:0000305}.
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DR EMBL; AP003712; BAD37587.1; -; Genomic_DNA.
DR EMBL; AP003712; BAD37588.1; -; Genomic_DNA.
DR EMBL; AP008212; BAF20166.1; -; Genomic_DNA.
DR EMBL; AP014962; BAS98942.1; -; Genomic_DNA.
DR EMBL; AP014962; BAS98944.1; -; Genomic_DNA.
DR EMBL; AK067261; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AK068985; BAG91197.1; -; mRNA.
DR RefSeq; XP_015643415.1; XM_015787929.1. [Q67W82-1]
DR AlphaFoldDB; Q67W82; -.
DR SMR; Q67W82; -.
DR STRING; 4530.OS06T0656500-01; -.
DR PaxDb; Q67W82; -.
DR PRIDE; Q67W82; -.
DR EnsemblPlants; Os06t0656500-01; Os06t0656500-01; Os06g0656500. [Q67W82-1]
DR EnsemblPlants; Os06t0656500-02; Os06t0656500-02; Os06g0656500. [Q67W82-2]
DR GeneID; 4341718; -.
DR Gramene; Os06t0656500-01; Os06t0656500-01; Os06g0656500. [Q67W82-1]
DR Gramene; Os06t0656500-02; Os06t0656500-02; Os06g0656500. [Q67W82-2]
DR KEGG; osa:4341718; -.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q67W82; -.
DR OMA; TPSDWAW; -.
DR OrthoDB; 683933at2759; -.
DR BRENDA; 6.2.1.12; 4460.
DR PlantReactome; R-OSA-1119316; Phenylpropanoid biosynthesis.
DR PlantReactome; R-OSA-1119531; Flavonoid biosynthesis.
DR PlantReactome; R-OSA-9627657; Regulation of leaf development.
DR UniPathway; UPA00372; UER00547.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 6.
DR Genevisible; Q67W82; OS.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0016207; F:4-coumarate-CoA ligase activity; IDA:UniProtKB.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016405; F:CoA-ligase activity; IBA:GO_Central.
DR GO; GO:0106290; F:trans-cinnamate-CoA ligase activity; IDA:UniProtKB.
DR GO; GO:0009809; P:lignin biosynthetic process; IMP:UniProtKB.
DR GO; GO:0009698; P:phenylpropanoid metabolic process; IDA:UniProtKB.
DR GO; GO:0010044; P:response to aluminum ion; IMP:UniProtKB.
DR Gene3D; 3.30.300.30; -; 1.
DR Gene3D; 3.40.50.12780; -; 1.
DR InterPro; IPR025110; AMP-bd_C.
DR InterPro; IPR045851; AMP-bd_C_sf.
DR InterPro; IPR020845; AMP-binding_CS.
DR InterPro; IPR000873; AMP-dep_Synth/Lig.
DR InterPro; IPR042099; ANL_N_sf.
DR Pfam; PF00501; AMP-binding; 1.
DR Pfam; PF13193; AMP-binding_C; 1.
DR PROSITE; PS00455; AMP_BINDING; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Cytoplasm; Ligase; Nucleotide-binding;
KW Phenylpropanoid metabolism; Reference proteome.
FT CHAIN 1..559
FT /note="4-coumarate--CoA ligase 4"
FT /id="PRO_0000351625"
FT REGION 271..340
FT /note="SBD1"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT REGION 341..408
FT /note="SBD2"
FT /evidence="ECO:0000250|UniProtKB:Q42524"
FT BINDING 198..206
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 246
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 341..346
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 345
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 429
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 444
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT BINDING 535
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:Q9SMT7"
FT VAR_SEQ 408..445
FT /note="YLNDPESTKNTIDKGGWLHTGDIGYVDDDDEIFIVDRL -> SISLSFFPLH
FT IIIGIISAKSIIHHLPRVYGHASACTTT (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_035525"
FT VAR_SEQ 446..559
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_035526"
FT MUTAGEN 395
FT /note="G->R: In ral1; reduced lignin content and increased
FT accumulation of 4-coumarate and ferulate in roots; confers
FT increased tolerance to aluminum."
FT /evidence="ECO:0000269|PubMed:32989851"
SQ SEQUENCE 559 AA; 60029 MW; DAC957A75C3E45BA CRC64;
MGSMAAAAEA AQEEETVVFR SKLPDIEIPS HLTLQAYCFE KLPEVAARPC LIDGQTGAVY
SYGEVEELSR RAAAGLRRLG VGKGDVVMSL LRNCPEFAFT FLGAARLGAA TTTANPFYTP
HEIHRQASAA GARVIVTEAC AVEKVRGFAA DRGIPVVAVD GDFDGCVGFG EAMLDASIEP
LDADEEVHPD DVVALPYSSG TTGLPKGVML THRSLVTSVA QQVDGENPNL YFRREDVVLC
LLPLFHIYSL NSVLLAGLRA GSAIVIMRKF DLGALVDLTR RHGVTVAPFV PPIVVEIAKS
PRVTADDLAS IRMVMSGAAP MGKDLQDAFM AKIPNAVLGQ GYGMTEAGPV LAMCLAFAKE
PFEVKSGSCG TVVRNAELKI VDPDTGATLG RNQSGEICIR GEQIMKGYLN DPESTKNTID
KGGWLHTGDI GYVDDDDEIF IVDRLKEIIK YKGFQVPPAE LEALLITHPD IKDAAVVPMI
DEIAGEVPVA FIVRIEGSAI SENEIKQFVA KEVVFYKRLN KVFFADSIPK SPSGKILRKD
LRAKLAAGIP TNDNTQLKS
