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Entry version 94 (16 Oct 2019)
Sequence version 1 (11 Oct 2004)
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Protein

Probable 4-coumarate--CoA ligase 4

Gene

4CL4

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score:

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at transcript leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: 3,4',5-trihydroxystilbene biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 3,4',5-trihydroxystilbene from trans-4-coumarate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Probable 4-coumarate--CoA ligase 2 (4CL2), Probable 4-coumarate--CoA ligase 5 (4CL5), Probable 4-coumarate--CoA ligase 3 (4CL3), Probable 4-coumarate--CoA ligase 4 (4CL4), Probable 4-coumarate--CoA ligase 1 (4CL1)
  2. no protein annotated in this organism
This subpathway is part of the pathway 3,4',5-trihydroxystilbene biosynthesis, which is itself part of Phytoalexin biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 3,4',5-trihydroxystilbene from trans-4-coumarate, the pathway 3,4',5-trihydroxystilbene biosynthesis and in Phytoalexin biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei429ATPBy similarity1
Binding sitei444ATPBy similarity1
Binding sitei535ATPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi198 – 206ATPBy similarity9
Nucleotide bindingi341 – 346ATPBy similarity6

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionLigase
Biological processPhenylpropanoid metabolism
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
6.2.1.12 4460

Reactome - a knowledgebase of biological pathways and processes for plant species

More...
PlantReactomei
R-OSA-1119316 Phenylpropanoid biosynthesis
R-OSA-1119531 Flavonoid biosynthesis
R-OSA-9627657 Regulation of leaf development

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA00372;UER00547

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Probable 4-coumarate--CoA ligase 4 (EC:6.2.1.12)
Short name:
4CL 4
Short name:
Os4CL4
Alternative name(s):
4-coumaroyl-CoA synthase 4
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:4CL4
Ordered Locus Names:Os06g0656500, LOC_Os06g44620
ORF Names:P0460H04.31-1, P0460H04.31-2
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiOryza sativa subsp. japonica (Rice)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri39947 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000059680 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 6

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00003516251 – 559Probable 4-coumarate--CoA ligase 4Add BLAST559

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
Q67W82

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q67W82 OS

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
4530.OS06T0656500-01

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q67W82

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni271 – 340SBD1Add BLAST70
Regioni341 – 408SBD2Add BLAST68

<p>This subsection of the ‘Family and domains’ section provides general information on the biological role of a domain. The term ‘domain’ is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

Both substrate-binding domains (SBD1 and SBD2) are involved in the substrate recognition, and are sufficient to confer the substrate specificity.

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1176 Eukaryota
COG0318 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000230009

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q67W82

KEGG Orthology (KO)

More...
KOi
K01904

Identification of Orthologs from Complete Genome Data

More...
OMAi
PAMVACW

Database of Orthologous Groups

More...
OrthoDBi
683933at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.50.12780, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR025110 AMP-bd_C
IPR020845 AMP-binding_CS
IPR000873 AMP-dep_Synth/Lig
IPR042099 AMP-dep_Synthh-like_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00501 AMP-binding, 1 hit
PF13193 AMP-binding_C, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00455 AMP_BINDING, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequences (2)i

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

This entry describes 2 <p>This subsection of the ‘Sequence’ section lists the alternative protein sequences (isoforms) that can be generated from the same gene by a single or by the combination of up to four biological events (alternative promoter usage, alternative splicing, alternative initiation and ribosomal frameshifting). Additionally, this section gives relevant information on each alternative protein isoform.<p><a href='/help/alternative_products' target='_top'>More...</a></p> isoformsi produced by alternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q67W82-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the <div> <p><b>What is the canonical sequence?</b><p><a href='/help/canonical_and_isoforms' target='_top'>More...</a></p>canonicali sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MGSMAAAAEA AQEEETVVFR SKLPDIEIPS HLTLQAYCFE KLPEVAARPC
60 70 80 90 100
LIDGQTGAVY SYGEVEELSR RAAAGLRRLG VGKGDVVMSL LRNCPEFAFT
110 120 130 140 150
FLGAARLGAA TTTANPFYTP HEIHRQASAA GARVIVTEAC AVEKVRGFAA
160 170 180 190 200
DRGIPVVAVD GDFDGCVGFG EAMLDASIEP LDADEEVHPD DVVALPYSSG
210 220 230 240 250
TTGLPKGVML THRSLVTSVA QQVDGENPNL YFRREDVVLC LLPLFHIYSL
260 270 280 290 300
NSVLLAGLRA GSAIVIMRKF DLGALVDLTR RHGVTVAPFV PPIVVEIAKS
310 320 330 340 350
PRVTADDLAS IRMVMSGAAP MGKDLQDAFM AKIPNAVLGQ GYGMTEAGPV
360 370 380 390 400
LAMCLAFAKE PFEVKSGSCG TVVRNAELKI VDPDTGATLG RNQSGEICIR
410 420 430 440 450
GEQIMKGYLN DPESTKNTID KGGWLHTGDI GYVDDDDEIF IVDRLKEIIK
460 470 480 490 500
YKGFQVPPAE LEALLITHPD IKDAAVVPMI DEIAGEVPVA FIVRIEGSAI
510 520 530 540 550
SENEIKQFVA KEVVFYKRLN KVFFADSIPK SPSGKILRKD LRAKLAAGIP

TNDNTQLKS
Length:559
Mass (Da):60,029
Last modified:October 11, 2004 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iDAC957A75C3E45BA
GO
Isoform 2 (identifier: Q67W82-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     408-445: YLNDPESTKN...DDEIFIVDRL → SISLSFFPLH...YGHASACTTT
     446-559: Missing.

Note: No experimental confirmation available.
Show »
Length:445
Mass (Da):47,220
Checksum:i546A33B5B6DBDFBA
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section describes the sequence of naturally occurring alternative protein isoform(s). The changes in the amino acid sequence may be due to alternative splicing, alternative promoter usage, alternative initiation, or ribosomal frameshifting.<p><a href='/help/var_seq' target='_top'>More...</a></p>Alternative sequenceiVSP_035525408 – 445YLNDP…IVDRL → SISLSFFPLHIIIGIISAKS IIHHLPRVYGHASACTTT in isoform 2. 1 PublicationAdd BLAST38
Alternative sequenceiVSP_035526446 – 559Missing in isoform 2. 1 PublicationAdd BLAST114

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
AP003712 Genomic DNA Translation: BAD37587.1
AP003712 Genomic DNA Translation: BAD37588.1
AP008212 Genomic DNA Translation: BAF20166.1
AP014962 Genomic DNA Translation: BAS98942.1
AP014962 Genomic DNA Translation: BAS98944.1
AK067261 mRNA No translation available.
AK068985 mRNA Translation: BAG91197.1

NCBI Reference Sequences

More...
RefSeqi
XP_015643415.1, XM_015787929.1 [Q67W82-1]

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
Os06t0656500-01; Os06t0656500-01; Os06g0656500 [Q67W82-1]
Os06t0656500-02; Os06t0656500-02; Os06g0656500 [Q67W82-2]

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4341718

Gramene; a comparative resource for plants

More...
Gramenei
Os06t0656500-01; Os06t0656500-01; Os06g0656500 [Q67W82-1]
Os06t0656500-02; Os06t0656500-02; Os06g0656500 [Q67W82-2]

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
osa:4341718

Keywords - Coding sequence diversityi

Alternative splicing

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP003712 Genomic DNA Translation: BAD37587.1
AP003712 Genomic DNA Translation: BAD37588.1
AP008212 Genomic DNA Translation: BAF20166.1
AP014962 Genomic DNA Translation: BAS98942.1
AP014962 Genomic DNA Translation: BAS98944.1
AK067261 mRNA No translation available.
AK068985 mRNA Translation: BAG91197.1
RefSeqiXP_015643415.1, XM_015787929.1 [Q67W82-1]

3D structure databases

SMRiQ67W82
ModBaseiSearch...

Protein-protein interaction databases

STRINGi4530.OS06T0656500-01

Proteomic databases

PaxDbiQ67W82

Genome annotation databases

EnsemblPlantsiOs06t0656500-01; Os06t0656500-01; Os06g0656500 [Q67W82-1]
Os06t0656500-02; Os06t0656500-02; Os06g0656500 [Q67W82-2]
GeneIDi4341718
GrameneiOs06t0656500-01; Os06t0656500-01; Os06g0656500 [Q67W82-1]
Os06t0656500-02; Os06t0656500-02; Os06g0656500 [Q67W82-2]
KEGGiosa:4341718

Phylogenomic databases

eggNOGiKOG1176 Eukaryota
COG0318 LUCA
HOGENOMiHOG000230009
InParanoidiQ67W82
KOiK01904
OMAiPAMVACW
OrthoDBi683933at2759

Enzyme and pathway databases

UniPathwayiUPA00372;UER00547
BRENDAi6.2.1.12 4460
PlantReactomeiR-OSA-1119316 Phenylpropanoid biosynthesis
R-OSA-1119531 Flavonoid biosynthesis
R-OSA-9627657 Regulation of leaf development

Gene expression databases

GenevisibleiQ67W82 OS

Family and domain databases

Gene3Di3.40.50.12780, 1 hit
InterProiView protein in InterPro
IPR025110 AMP-bd_C
IPR020845 AMP-binding_CS
IPR000873 AMP-dep_Synth/Lig
IPR042099 AMP-dep_Synthh-like_sf
PfamiView protein in Pfam
PF00501 AMP-binding, 1 hit
PF13193 AMP-binding_C, 1 hit
PROSITEiView protein in PROSITE
PS00455 AMP_BINDING, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry namei4CL4_ORYSJ
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q67W82
Secondary accession number(s): B7EFQ0, Q67W81
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 14, 2008
Last sequence update: October 11, 2004
Last modified: October 16, 2019
This is version 94 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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