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Entry version 93 (07 Apr 2021)
Sequence version 1 (17 Oct 2006)
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Protein

Pyruvate decarboxylase 1

Gene

PDC1

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%5Fsection">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 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei67SubstrateBy similarity1
Binding sitei154SubstrateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi482MagnesiumBy similarity1
Metal bindingi509MagnesiumBy similarity1
Metal bindingi511Magnesium; via carbonyl oxygenBy similarity1
Binding sitei515SubstrateBy similarity1

<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

<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 functionDecarboxylase, Lyase
LigandMagnesium, Metal-binding, Thiamine pyrophosphate

Enzyme and pathway databases

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

More...
PlantReactomei
R-OSA-1119460, Isoleucine biosynthesis from threonine
R-OSA-1119486, IAA biosynthesis I
R-OSA-1119600, Valine biosynthesis

<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%5Fand%5Ftaxonomy%5Fsection">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:
Pyruvate decarboxylase 1 (EC:4.1.1.1)
Short name:
PDC
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:PDC1
Ordered Locus Names:Os05g0469600, LOC_Os05g39310
ORF Names:OsJ_018109, OSJNBa0052E20.2
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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%5Fand%5Ftaxonomy%5Fsection">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
  • UP000007752 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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 5
  • UP000059680 Componenti: Chromosome 5
  • UP000000763 Componenti: Chromosome 5

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000907791 – 605Pyruvate decarboxylase 1Add BLAST605

Proteomic databases

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

More...
PaxDbi
Q0DHF6

PRoteomics IDEntifications database

More...
PRIDEi
Q0DHF6

<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

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q0DHF6, differential

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
Q0DHF6, 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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotetramer.

Curated

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
4530.OS05T0469600-01

<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
Q0DHF6

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>Regioni432 – 514Thiamine pyrophosphate bindingAdd BLAST83

<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

Belongs to the TPP enzyme family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG1184, Eukaryota

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_013748_0_2_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
Q0DHF6

Identification of Orthologs from Complete Genome Data

More...
OMAi
YLSIGMA

Database of Orthologous Groups

More...
OrthoDBi
560466at2759

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR029035, DHS-like_NAD/FAD-binding_dom
IPR029061, THDP-binding
IPR012000, Thiamin_PyroP_enz_cen_dom
IPR012001, Thiamin_PyroP_enz_TPP-bd_dom
IPR012110, TPP_enzyme
IPR011766, TPP_enzyme-bd_C

The PANTHER Classification System

More...
PANTHERi
PTHR43452, PTHR43452, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF02775, TPP_enzyme_C, 1 hit
PF00205, TPP_enzyme_M, 1 hit
PF02776, TPP_enzyme_N, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF036565, Pyruvt_ip_decrb, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF52467, SSF52467, 1 hit
SSF52518, SSF52518, 2 hits

<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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

Q0DHF6-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MELALVGNPS NGVAKPSCNS VGSLPVVSSN AVINPPVTSA AGATLGRHLA
60 70 80 90 100
RRLVQIGATD VFAVPGDFNL TLLDYLIAEP GLKLIGCCNE LNAGYAADGY
110 120 130 140 150
ARARGVGACA VTFTVGGLSV LNAIAGAYSE NLPVICIVGG PNSNDYGTNR
160 170 180 190 200
ILHHTIGLPD FSQELRCFQT ITCYQAVINN LDDAHEQIDT AIATALRESK
210 220 230 240 250
PVYISVGCNL AGLSHPTFSR EPVPLFISPR LSNKANLEYA VEAAADFLNK
260 270 280 290 300
AVKPVMVGGP KIRVAKAKKA FAGIAESSGY PFAVMPSAKG LVPEHHPRFI
310 320 330 340 350
GTYWGAVSTT FCAEIVESAD AYLFAGPIFN DYSSVGYSLL LKREKAVIVQ
360 370 380 390 400
PDRVVVGNGP AFGCILMTEF LDALAKRLDR NTTAYDNYRR IFIPDREPPN
410 420 430 440 450
GQPDEPLRVN ILFKHIKEML SGDTAVIAET GDSWFNCQKL RLPEGCGYEF
460 470 480 490 500
QMQYGSIGWS VGATLGYAQA AKDKRVISCI GDGSFQMTAQ DVSTMLRCGQ
510 520 530 540 550
KSIIFLINNG GYTIEVEIHD GPYNVIKNWD YTGLIDAIHN SDGNCWTKKV
560 570 580 590 600
RTEEELIEAI ATATGAKKDC LCFIEIIVHK DDTSKELLEW GSRVSAANSR

PPNPQ
Length:605
Mass (Da):65,155
Last modified:October 17, 2006 - 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:i78406A557955301B
GO

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
AC121364 Genomic DNA Translation: AAT93945.1
AP008211 Genomic DNA Translation: BAF17717.1
AP014961 Genomic DNA Translation: BAS94476.1
CM000142 Genomic DNA Translation: EAZ34626.1
AK100678 mRNA No translation available.

NCBI Reference Sequences

More...
RefSeqi
XP_015637741.1, XM_015782255.1

Genome annotation databases

Ensembl plant genome annotation project

More...
EnsemblPlantsi
Os05t0469600-01; Os05t0469600-01; Os05g0469600

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
4339066

Gramene; a comparative resource for plants

More...
Gramenei
Os05t0469600-01; Os05t0469600-01; Os05g0469600

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
osa:4339066

<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
AC121364 Genomic DNA Translation: AAT93945.1
AP008211 Genomic DNA Translation: BAF17717.1
AP014961 Genomic DNA Translation: BAS94476.1
CM000142 Genomic DNA Translation: EAZ34626.1
AK100678 mRNA No translation available.
RefSeqiXP_015637741.1, XM_015782255.1

3D structure databases

SMRiQ0DHF6
ModBaseiSearch...

Protein-protein interaction databases

STRINGi4530.OS05T0469600-01

Proteomic databases

PaxDbiQ0DHF6
PRIDEiQ0DHF6

Genome annotation databases

EnsemblPlantsiOs05t0469600-01; Os05t0469600-01; Os05g0469600
GeneIDi4339066
GrameneiOs05t0469600-01; Os05t0469600-01; Os05g0469600
KEGGiosa:4339066

Phylogenomic databases

eggNOGiKOG1184, Eukaryota
HOGENOMiCLU_013748_0_2_1
InParanoidiQ0DHF6
OMAiYLSIGMA
OrthoDBi560466at2759

Enzyme and pathway databases

PlantReactomeiR-OSA-1119460, Isoleucine biosynthesis from threonine
R-OSA-1119486, IAA biosynthesis I
R-OSA-1119600, Valine biosynthesis

Gene expression databases

ExpressionAtlasiQ0DHF6, differential
GenevisibleiQ0DHF6, OS

Family and domain databases

InterProiView protein in InterPro
IPR029035, DHS-like_NAD/FAD-binding_dom
IPR029061, THDP-binding
IPR012000, Thiamin_PyroP_enz_cen_dom
IPR012001, Thiamin_PyroP_enz_TPP-bd_dom
IPR012110, TPP_enzyme
IPR011766, TPP_enzyme-bd_C
PANTHERiPTHR43452, PTHR43452, 1 hit
PfamiView protein in Pfam
PF02775, TPP_enzyme_C, 1 hit
PF00205, TPP_enzyme_M, 1 hit
PF02776, TPP_enzyme_N, 1 hit
PIRSFiPIRSF036565, Pyruvt_ip_decrb, 1 hit
SUPFAMiSSF52467, SSF52467, 1 hit
SSF52518, SSF52518, 2 hits

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 nameiPDC1_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: Q0DHF6
Secondary accession number(s): P51847, Q6AUJ9
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 11, 2007
Last sequence update: October 17, 2006
Last modified: April 7, 2021
This is version 93 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

Reference proteome

Documents

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