ID 4CLL3_ORYSJ Reviewed; 591 AA.
AC Q6YYZ2; C7J6B0;
DT 14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 27-MAR-2024, entry version 96.
DE RecName: Full=4-coumarate--CoA ligase-like 3;
DE EC=6.2.1.12 {ECO:0000250|UniProtKB:O24146};
GN Name=4CLL3; OrderedLocusNames=Os08g0143300, LOC_Os08g04770;
GN ORFNames=P0025F03.16, P0473D02.38;
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 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).
CC -!- FUNCTION: Carboxylate--CoA ligase that may use 4-coumarate as
CC substrate. Follows a two-step reaction mechanism, wherein the
CC carboxylate substrate first undergoes adenylation by ATP, followed by a
CC thioesterification in the presence of CoA to yield the final CoA
CC thioester. {ECO:0000250|UniProtKB:O24146}.
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:0000250|UniProtKB:O24146};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:19642;
CC Evidence={ECO:0000250|UniProtKB:O24146};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(E)-4-coumarate + ATP + H(+) = (E)-4-coumaroyl-AMP +
CC diphosphate; Xref=Rhea:RHEA:72419, ChEBI:CHEBI:12876,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:192348; Evidence={ECO:0000250|UniProtKB:O24146};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:72420;
CC Evidence={ECO:0000250|UniProtKB:O24146};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(E)-4-coumaroyl-AMP + CoA = (E)-4-coumaroyl-CoA + AMP + H(+);
CC Xref=Rhea:RHEA:72423, ChEBI:CHEBI:15378, ChEBI:CHEBI:57287,
CC ChEBI:CHEBI:85008, ChEBI:CHEBI:192348, ChEBI:CHEBI:456215;
CC Evidence={ECO:0000250|UniProtKB:O24146};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:72424;
CC Evidence={ECO:0000250|UniProtKB:O24146};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:O24146};
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; AP004381; BAD17022.1; -; Genomic_DNA.
DR EMBL; AP005542; BAD13196.1; -; Genomic_DNA.
DR EMBL; AP008214; BAH94104.1; -; Genomic_DNA.
DR EMBL; AP014964; BAT03799.1; -; Genomic_DNA.
DR RefSeq; XP_015650198.1; XM_015794712.1.
DR AlphaFoldDB; Q6YYZ2; -.
DR SMR; Q6YYZ2; -.
DR STRING; 39947.Q6YYZ2; -.
DR PaxDb; 39947-Q6YYZ2; -.
DR EnsemblPlants; Os08t0143300-00; Os08t0143300-00; Os08g0143300.
DR GeneID; 9269113; -.
DR Gramene; Os08t0143300-00; Os08t0143300-00; Os08g0143300.
DR KEGG; osa:9269113; -.
DR eggNOG; KOG1176; Eukaryota.
DR HOGENOM; CLU_000022_59_2_1; -.
DR InParanoid; Q6YYZ2; -.
DR OMA; HDRTIND; -.
DR OrthoDB; 1404660at2759; -.
DR PlantReactome; R-OSA-1119316; Phenylpropanoid biosynthesis.
DR PlantReactome; R-OSA-1119531; Flavonoid biosynthesis.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR Genevisible; Q6YYZ2; OS.
DR GO; GO:0005777; C:peroxisome; IBA:GO_Central.
DR GO; GO:0016207; F:4-coumarate-CoA ligase activity; IEA:UniProt.
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; IEA:UniProt.
DR GO; GO:0009698; P:phenylpropanoid metabolic process; IEA:UniProt.
DR GO; GO:0006744; P:ubiquinone biosynthetic process; IBA:GO_Central.
DR CDD; cd05904; 4CL; 1.
DR Gene3D; 3.30.300.30; -; 1.
DR Gene3D; 3.40.50.12780; N-terminal domain of ligase-like; 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_com.
DR InterPro; IPR042099; ANL_N_sf.
DR PANTHER; PTHR24096:SF261; 4-COUMARATE--COA LIGASE-LIKE 6; 1.
DR PANTHER; PTHR24096; LONG-CHAIN-FATTY-ACID--COA LIGASE; 1.
DR Pfam; PF00501; AMP-binding; 1.
DR Pfam; PF13193; AMP-binding_C; 1.
DR SUPFAM; SSF56801; Acetyl-CoA synthetase-like; 1.
DR PROSITE; PS00455; AMP_BINDING; 1.
PE 3: Inferred from homology;
KW ATP-binding; Ligase; Magnesium; Nucleotide-binding; Reference proteome.
FT CHAIN 1..591
FT /note="4-coumarate--CoA ligase-like 3"
FT /id="PRO_0000351629"
FT REGION 303..375
FT /note="SBD1"
FT REGION 376..440
FT /note="SBD2"
FT BINDING 228
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 229
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 230
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 231
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 232
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 236
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 280
FT /ligand="(E)-4-coumaroyl-AMP"
FT /ligand_id="ChEBI:CHEBI:192348"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 301
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 353
FT /ligand="(E)-4-coumaroyl-AMP"
FT /ligand_id="ChEBI:CHEBI:192348"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 375
FT /ligand="(E)-4-coumaroyl-AMP"
FT /ligand_id="ChEBI:CHEBI:192348"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 375
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 376
FT /ligand="(E)-4-coumaroyl-AMP"
FT /ligand_id="ChEBI:CHEBI:192348"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 376
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 380
FT /ligand="(E)-4-coumaroyl-AMP"
FT /ligand_id="ChEBI:CHEBI:192348"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 380
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 459
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 474
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 476
FT /ligand="(E)-4-coumaroyl-AMP"
FT /ligand_id="ChEBI:CHEBI:192348"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 480
FT /ligand="(E)-4-coumaroyl-AMP"
FT /ligand_id="ChEBI:CHEBI:192348"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 482
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 483
FT /ligand="CoA"
FT /ligand_id="ChEBI:CHEBI:57287"
FT /evidence="ECO:0000250|UniProtKB:O24146"
FT BINDING 565
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O24146"
SQ SEQUENCE 591 AA; 62081 MW; B128A79F1B0934C1 CRC64;
MQRDAIAAAR NAGCSSGRIS QPPPPPFYSA ATGIYSSIHP PVALPTDPSL TLVAHLFARL
PLADPGAPTL VDAATASAVS RADLRRLVAS LAAGLRRRHG VRKGSVVLLL LPNSVAFPVS
FLAVLAAGAV ATTMNPSSSP AEIAAQARAT GACLVLASRD GAARLPPLAA PVVLVPEILD
HSAAADDGDD DQRVFAAFRA MLDGGGGDGT ETAVPVVGQD DAVAILYSSG TSGRSKGVVL
THRNLIAMTE LFVRFEASQY HARGARENVY MAALPMSHVY GLSLFAVGLL SIGATVVVMR
RFDAGDAVAA IGRYKVTHMP LVPPIMAAMV RAAAAGGVPP SQVASLVQVS CGAAPITAAL
IHEFLQAFPH VDFIQGYGMT ESTAVGTRGF NTSKHKKYTS VGLLAPNMHA KIVHLESSSC
LPPGFSGELW LHGPGIMKGY LSDDDDACTR KDGWLRTGDI AYFDLDGYLY IVGRLKDTIK
YKGFQIAPGD LEEVLIHHPE ILDVAVTSAE DEEAGEIPVA FVVRRSGSNL SCKQVMEYVA
KQVAPYKRVR KVVFVEAIPK SPAGKVLRRL LRNSHDTAAA ATSSCSISSK L
//
