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Entry version 117 (16 Oct 2019)
Sequence version 2 (27 Sep 2005)
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Protein

Probable 4-coumarate--CoA ligase 2

Gene

4CL2

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 sitei450ATPBy similarity1
Binding sitei465ATPBy similarity1
Binding sitei556ATPBy 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 bindingi219 – 227ATPBy similarity9
Nucleotide bindingi362 – 367ATPBy 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-1119418 Suberin biosynthesis
R-OSA-1119531 Flavonoid biosynthesis

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 2 (EC:6.2.1.12)
Short name:
4CL 2
Short name:
Os4CL2
Alternative name(s):
4-coumaroyl-CoA synthase 2
<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:4CL2
Synonyms:4CL.2
Ordered Locus Names:Os02g0697400, LOC_Os02g46970
ORF Names:P0459B01.4-1, P0666E12.12-1
<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 2

<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_00001930321 – 569Probable 4-coumarate--CoA ligase 2Add BLAST569

Proteomic databases

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

More...
PaxDbi
Q42982

PRoteomics IDEntifications database

More...
PRIDEi
Q42982

<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
Q42982 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.OS02T0697400-01

<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
Q42982

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>Regioni292 – 361SBD1Add BLAST70
Regioni362 – 429SBD2Add 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
Q42982

KEGG Orthology (KO)

More...
KOi
K01904

Identification of Orthologs from Complete Genome Data

More...
OMAi
GLMQDWP

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>Sequencei

<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.

Q42982-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MITVAAPEAQ PQVAAAVDEA PPEAVTVFRS KLPDIDIPSH LPLHEYCFAR
60 70 80 90 100
AAELPDAPCL IAAATGRTYT FAETRLLCRR AAAALHRLGV GHGDRVMVLL
110 120 130 140 150
QNCVEFAVAF FAASFLGAVT TAANPFCTPQ EIHKQFKASG VKLILTQSVY
160 170 180 190 200
VDKLRQHEAF PRIDACTVGD DTLTVITIDD DEATPEGCLP FWDLIADADE
210 220 230 240 250
GSVPEVAISP DDPVALPFSS GTTGLPKGVV LTHRSVVSGV AQQVDGENPN
260 270 280 290 300
LHMGAGDVAL CVLPLFHIFS LNSVLLCAVR AGAAVALMPR FEMGAMLGAI
310 320 330 340 350
ERWRVTVAAV VPPLVLALAK NPFVERHDLS SIRIVLSGAA PLGKELEDAL
360 370 380 390 400
RARLPQAIFG QGYGMTEAGP VLSMCPAFAK EPTPAKSGSC GTVVRNAELK
410 420 430 440 450
VVDPDTGFSL GRNLPGEICI RGPQIMKGYL NDPEATAATI DVEGWLHTGD
460 470 480 490 500
IGYVDDDDEV FIVDRVKELI KFKGFQVPPA ELESLLIAHP SIADAAVVPQ
510 520 530 540 550
KDDVAGEVPV AFVVRAADSD ITEESIKEFI SKQVVFYKRL HKVHFIHAIP
560
KSASGKILRR ELRAKLAAC
Length:569
Mass (Da):60,815
Last modified:September 27, 2005 - v2
<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:i2A1A1FF3CF7FEC91
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Sequence’ section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti138A → G in AAA69580 (Ref. 1) Curated1
Sequence conflicti186 – 187EG → KA in AAA69580 (Ref. 1) Curated2
Sequence conflicti226P → A in AAA69580 (Ref. 1) Curated1
Sequence conflicti242 – 243QQ → HE in AAA69580 (Ref. 1) Curated2
Sequence conflicti277 – 283CAVRAGA → SRVRPAP in AAA69580 (Ref. 1) Curated7
Sequence conflicti308A → G in AAA69580 (Ref. 1) Curated1
Sequence conflicti316L → V in AAA69580 (Ref. 1) Curated1
Sequence conflicti450D → N in AAA69580 (Ref. 1) Curated1
Sequence conflicti493A → R in AAA69580 (Ref. 1) Curated1

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
L43362 mRNA Translation: AAA69580.1
AP004778 Genomic DNA Translation: BAD07859.1
AP005868 Genomic DNA Translation: BAD08175.1
AP008208 Genomic DNA Translation: BAF09733.1
AP014958 Genomic DNA Translation: BAS80426.1
AK105636 mRNA Translation: BAG97321.1

Protein sequence database of the Protein Information Resource

More...
PIRi
T03390

NCBI Reference Sequences

More...
RefSeqi
XP_015624111.1, XM_015768625.1

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
Os02t0697400-01; Os02t0697400-01; Os02g0697400

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4330407

Gramene; a comparative resource for plants

More...
Gramenei
Os02t0697400-01; Os02t0697400-01; Os02g0697400

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
osa:4330407

<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
L43362 mRNA Translation: AAA69580.1
AP004778 Genomic DNA Translation: BAD07859.1
AP005868 Genomic DNA Translation: BAD08175.1
AP008208 Genomic DNA Translation: BAF09733.1
AP014958 Genomic DNA Translation: BAS80426.1
AK105636 mRNA Translation: BAG97321.1
PIRiT03390
RefSeqiXP_015624111.1, XM_015768625.1

3D structure databases

SMRiQ42982
ModBaseiSearch...

Protein-protein interaction databases

STRINGi4530.OS02T0697400-01

Proteomic databases

PaxDbiQ42982
PRIDEiQ42982

Genome annotation databases

EnsemblPlantsiOs02t0697400-01; Os02t0697400-01; Os02g0697400
GeneIDi4330407
GrameneiOs02t0697400-01; Os02t0697400-01; Os02g0697400
KEGGiosa:4330407

Phylogenomic databases

eggNOGiKOG1176 Eukaryota
COG0318 LUCA
HOGENOMiHOG000230009
InParanoidiQ42982
KOiK01904
OMAiGLMQDWP
OrthoDBi683933at2759

Enzyme and pathway databases

UniPathwayiUPA00372;UER00547
BRENDAi6.2.1.12 4460
PlantReactomeiR-OSA-1119316 Phenylpropanoid biosynthesis
R-OSA-1119418 Suberin biosynthesis
R-OSA-1119531 Flavonoid biosynthesis

Gene expression databases

GenevisibleiQ42982 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 namei4CL2_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: Q42982
Secondary accession number(s): B7EY74, Q0DYF5, Q6YUH6
<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: January 11, 2001
Last sequence update: September 27, 2005
Last modified: October 16, 2019
This is version 117 of the entry and version 2 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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