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Protein

6-phosphogluconate dehydrogenase, decarboxylating 2, chloroplastic

Gene

pgdP

Organism
Spinacia oleracea (Spinach)
Status
Reviewed-Annotation score:

Annotation score:5 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 protein 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

Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO2, with concomitant reduction of NADP to NADPH.1 Publication

<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 ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

  1. KM=40 µM for 6-phosphoglutanate1 Publication
  2. KM=6 µM for NADP1 Publication

    <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: pentose phosphate pathway

    This protein is involved in step 3 of the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage).
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase (SOVF_162250), Glucose-6-phosphate 1-dehydrogenase (SOVF_004890), Glucose-6-phosphate 1-dehydrogenase (SOVF_183760), Glucose-6-phosphate 1-dehydrogenase (G6PD), Glucose-6-phosphate 1-dehydrogenase, chloroplastic (G6PD)
    2. no protein annotated in this organism
    3. 6-phosphogluconate dehydrogenase, decarboxylating (SOVF_128490), 6-phosphogluconate dehydrogenase, decarboxylating (SOVF_090000), 6-phosphogluconate dehydrogenase, decarboxylating 1 (pgdC), 6-phosphogluconate dehydrogenase, decarboxylating 2, chloroplastic (pgdP)
    This subpathway is part of the pathway pentose phosphate pathway, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage), the pathway pentose phosphate pathway and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ 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 sitei150NADPBy similarity1
    Binding sitei150SubstrateBy similarity1
    <p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei230Proton acceptorBy similarity1
    Active sitei237Proton donorBy similarity1
    Binding sitei238SubstrateBy similarity1
    Binding sitei308Substrate; via amide nitrogenBy similarity1
    Binding sitei335SubstrateBy similarity1
    Binding sitei500Substrate; shared with dimeric partnerBy similarity1
    Binding sitei506Substrate; shared with dimeric partnerBy similarity1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ 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 bindingi55 – 60NADPBy similarity6
    Nucleotide bindingi78 – 80NADPBy similarity3
    Nucleotide bindingi122 – 124NADPBy similarity3

    <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

    • NADP binding Source: InterPro
    • phosphogluconate dehydrogenase (decarboxylating) activity Source: UniProtKB

    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 functionOxidoreductase
    Biological processGluconate utilization, Pentose shunt
    LigandNADP

    Enzyme and pathway databases

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    Q94KU2

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

    More...
    UniPathwayi
    UPA00115;UER00410

    <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:
    6-phosphogluconate dehydrogenase, decarboxylating 2, chloroplastic (EC:1.1.1.44)
    <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:pgdP
    <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>OrganismiSpinacia oleracea (Spinach)
    <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 identifieri3562 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaeCaryophyllalesChenopodiaceaeChenopodioideaeAnserineaeSpinacia

    <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

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Chloroplast, Plastid

    <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 transit peptide.<p><a href='/help/transit' target='_top'>More...</a></p>Transit peptidei1 – 44ChloroplastSequence analysisAdd BLAST44
    <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_000042110445 – 5376-phosphogluconate dehydrogenase, decarboxylating 2, chloroplasticAdd BLAST493

    Proteomic databases

    PRoteomics IDEntifications database

    More...
    PRIDEi
    Q94KU2

    <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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer.1 Publication

    <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

    Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

    More...
    ProteinModelPortali
    Q94KU2

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

    More...
    SMRi
    Q94KU2

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    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>Regioni176 – 178Substrate bindingBy similarity3
    Regioni233 – 234Substrate bindingBy similarity2

    <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

    Keywords - Domaini

    Transit peptide

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    1.10.1040.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR008927 6-PGluconate_DH-like_C_sf
    IPR013328 6PGD_dom2
    IPR006114 6PGDH_C
    IPR006113 6PGDH_Gnd/GntZ
    IPR006115 6PGDH_NADP-bd
    IPR036291 NAD(P)-bd_dom_sf
    IPR006183 Pgluconate_DH

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR11811 PTHR11811, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00393 6PGD, 1 hit
    PF03446 NAD_binding_2, 1 hit

    Protein Motif fingerprint database; a protein domain database

    More...
    PRINTSi
    PR00076 6PGDHDRGNASE

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM01350 6PGD, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF48179 SSF48179, 1 hit
    SSF51735 SSF51735, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00873 gnd, 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>.<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.

    <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 in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

    Q94KU2-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MRSEVPSSTS PSFLSPPFIH LPLLSLSSPT PLPHSSSSTF SLFSTMAASQ
    60 70 80 90 100
    IGLVGLAVMG QNLALNIAEK GFPISVYNRT ASKVDETLDR AKSEGDLPLS
    110 120 130 140 150
    GHYTPRDFVL SIERPRSIVI LVKAGSPVDQ TIASLASFME PGDTIIDGGN
    160 170 180 190 200
    EWYQNTERRL SDAHSNGLLY LGMGVSGGEE GARFGPSLMP GGDFQAYDNI
    210 220 230 240 250
    QHILKKVAAQ VDDGPCVTYI GEGGSGNFVK MVHNGIEYGD MQLISEAYDV
    260 270 280 290 300
    LKNVGGLSNE ELGQIFDEWN KSELESFLVE ITADIFKVKD DLADGGLVDK
    310 320 330 340 350
    ILDKTGMKGT GKWTVQQAAE LSVAAPTIAA SLDCRYLSGL KEERENAAKI
    360 370 380 390 400
    LEAAGMKEEV NAIRGGVDKK RLIDDVRQAL YASKICSYAQ GMNLLRAKSA
    410 420 430 440 450
    EMGWDLNLGE LARIWKGGCI IRAVFLDSIK QAYQRNPNLA SLVVDPEFAK
    460 470 480 490 500
    EMVQRQAAWR RVVGLAVSAG ISTPGMCASL AYFDTYRRAR LPANLVQAQR
    510 520 530
    DYFGAHTYER VDLPGSYHTE WSKLARKSDP NVAAALH
    Length:537
    Mass (Da):58,293
    Last modified:December 1, 2001 - 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:i8AB4D8F926B1DA71
    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
    AF295670 mRNA Translation: AAK49897.1

    <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
    AF295670 mRNA Translation: AAK49897.1

    3D structure databases

    ProteinModelPortaliQ94KU2
    SMRiQ94KU2
    ModBaseiSearch...
    MobiDBiSearch...

    Proteomic databases

    PRIDEiQ94KU2

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayi
    UPA00115;UER00410

    SABIO-RKiQ94KU2

    Family and domain databases

    Gene3Di1.10.1040.10, 1 hit
    InterProiView protein in InterPro
    IPR008927 6-PGluconate_DH-like_C_sf
    IPR013328 6PGD_dom2
    IPR006114 6PGDH_C
    IPR006113 6PGDH_Gnd/GntZ
    IPR006115 6PGDH_NADP-bd
    IPR036291 NAD(P)-bd_dom_sf
    IPR006183 Pgluconate_DH
    PANTHERiPTHR11811 PTHR11811, 1 hit
    PfamiView protein in Pfam
    PF00393 6PGD, 1 hit
    PF03446 NAD_binding_2, 1 hit
    PRINTSiPR00076 6PGDHDRGNASE
    SMARTiView protein in SMART
    SM01350 6PGD, 1 hit
    SUPFAMiSSF48179 SSF48179, 1 hit
    SSF51735 SSF51735, 1 hit
    TIGRFAMsiTIGR00873 gnd, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    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 namei6PGD2_SPIOL
    <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: Q94KU2
    <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: February 6, 2013
    Last sequence update: December 1, 2001
    Last modified: December 5, 2018
    This is version 78 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

    Direct protein sequencing

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
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