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Entry version 137 (13 Nov 2019)
Sequence version 1 (01 May 1992)
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Protein

Pyridoxine 4-dehydrogenase

Gene

pdxI

Organism
Escherichia coli (strain K12)
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 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 NAD(P)H-dependent reduction of pyridoxal to pyridoxine in vitro. Is not able to reduce 4-pyridoxate, and to oxidize pyridoxine or pyridoxamine (PubMed:27941785). Has Kemp eliminase activity towards the non-physiological substrate 5-nitrobenzisoxazole, producing 4-nitro-2-cyanophenol; this activity is not considered to be physiologically relevant (PubMed:21332126).2 Publications

<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

kcat is 0.11 sec(-1) for the Kemp eliminase activity towards 5-nitrobenzisoxazole.1 Publication
  1. KM=270 µM for 5-nitrobenzisoxazole1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> 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 sitei59Proton donorBy 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 bindingi210 – 218NADPBy similarity9

    <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 functionOxidoreductase
    LigandNAD, NADP

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:EG11309-MONOMER
    ECOL316407:JW1403-MONOMER
    MetaCyc:EG11309-MONOMER

    <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:
    Pyridoxine 4-dehydrogenase1 Publication (EC:1.1.1.651 Publication)
    <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:pdxI1 Publication
    Synonyms:ydbCImported
    Ordered Locus Names:b1406, JW1403
    <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>OrganismiEscherichia coli (strain K12)
    <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 identifieri83333 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    <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
    • UP000000318 <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
    • UP000000625 Componenti: Chromosome

    <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

    GO - Cellular componenti

    <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_00000703931 – 286Pyridoxine 4-dehydrogenaseAdd BLAST286

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...
    jPOSTi
    P25906

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

    More...
    PaxDbi
    P25906

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P25906

    2D gel databases

    Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

    More...
    SWISS-2DPAGEi
    P25906

    <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

    The Biological General Repository for Interaction Datasets (BioGrid)

    More...
    BioGridi
    4263019, 15 interactors

    Database of interacting proteins

    More...
    DIPi
    DIP-11632N

    Protein interaction database and analysis system

    More...
    IntActi
    P25906, 4 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    511145.b1406

    <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
    P25906

    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

    <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
    ENOG4107S5I Bacteria
    ENOG410XRV3 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000250284

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    P25906

    KEGG Orthology (KO)

    More...
    KOi
    K05275

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P25906

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd06660 Aldo_ket_red, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.20.20.100, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR023210 NADP_OxRdtase_dom
    IPR036812 NADP_OxRdtase_dom_sf

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00248 Aldo_ket_red, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51430 SSF51430, 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.

    P25906-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MSSNTFTLGT KSVNRLGYGA MQLAGPGVFG PPRDRHVAIT VLREALALGV
    60 70 80 90 100
    NHIDTSDFYG PHVTNQIIRE ALYPYSDDLT IVTKIGARRG EDASWLPAFS
    110 120 130 140 150
    PAELQKAVHD NLRNLGLDVL DVVNLRVMMG DGHGPAEGSI EASLTVLAEM
    160 170 180 190 200
    QQQGLVKHIG LSNVTPTQVA EARKIAEIVC VQNEYNIAHR ADDAMIDALA
    210 220 230 240 250
    HDGIAYVPFF PLGGFTPLQS STLSDVAASL GATPMQVALA WLLQRSPNIL
    260 270 280
    LIPGTSSVAH LRENMAAEKL HLSEEVLSTL DGISRE
    Length:286
    Mass (Da):30,706
    Last modified:May 1, 1992 - 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:i82B587AEA9115EF9
    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
    X62680 Genomic DNA Translation: CAA44553.1
    U00096 Genomic DNA Translation: AAC74488.1
    AP009048 Genomic DNA Translation: BAA15021.1
    X97452 Genomic DNA Translation: CAA66103.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    A48399

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_415924.1, NC_000913.3
    WP_000097801.1, NZ_SSZK01000021.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC74488; AAC74488; b1406
    BAA15021; BAA15021; BAA15021

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    945980

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW1403
    eco:b1406

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|1411691.4.peg.865

    <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
    X62680 Genomic DNA Translation: CAA44553.1
    U00096 Genomic DNA Translation: AAC74488.1
    AP009048 Genomic DNA Translation: BAA15021.1
    X97452 Genomic DNA Translation: CAA66103.1
    PIRiA48399
    RefSeqiNP_415924.1, NC_000913.3
    WP_000097801.1, NZ_SSZK01000021.1

    3D structure databases

    SMRiP25906
    ModBaseiSearch...

    Protein-protein interaction databases

    BioGridi4263019, 15 interactors
    DIPiDIP-11632N
    IntActiP25906, 4 interactors
    STRINGi511145.b1406

    2D gel databases

    SWISS-2DPAGEiP25906

    Proteomic databases

    jPOSTiP25906
    PaxDbiP25906
    PRIDEiP25906

    Protocols and materials databases

    The DNASU plasmid repository

    More...
    DNASUi
    945980

    Genome annotation databases

    EnsemblBacteriaiAAC74488; AAC74488; b1406
    BAA15021; BAA15021; BAA15021
    GeneIDi945980
    KEGGiecj:JW1403
    eco:b1406
    PATRICifig|1411691.4.peg.865

    Organism-specific databases

    EchoBASE - an integrated post-genomic database for E. coli

    More...
    EchoBASEi
    EB1285

    Phylogenomic databases

    eggNOGiENOG4107S5I Bacteria
    ENOG410XRV3 LUCA
    HOGENOMiHOG000250284
    InParanoidiP25906
    KOiK05275
    PhylomeDBiP25906

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11309-MONOMER
    ECOL316407:JW1403-MONOMER
    MetaCyc:EG11309-MONOMER

    Miscellaneous databases

    Protein Ontology

    More...
    PROi
    PR:P25906

    Family and domain databases

    CDDicd06660 Aldo_ket_red, 1 hit
    Gene3Di3.20.20.100, 1 hit
    InterProiView protein in InterPro
    IPR023210 NADP_OxRdtase_dom
    IPR036812 NADP_OxRdtase_dom_sf
    PfamiView protein in Pfam
    PF00248 Aldo_ket_red, 1 hit
    SUPFAMiSSF51430 SSF51430, 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 nameiPDXI_ECOLI
    <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: P25906
    <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: May 1, 1992
    Last sequence update: May 1, 1992
    Last modified: November 13, 2019
    This is version 137 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 programProkaryotic 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
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