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Entry version 30 (18 Sep 2019)
Sequence version 1 (16 Apr 2014)
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Protein

Pyridoxine 5'-phosphate oxidase

Gene

pdxH

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
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 oxidation of pyridoxine 5'-phosphate (PNP) into pyridoxal 5'-phosphate (PLP). Unlike many PNPOx enzymes, Rv2607 does not recognize pyridoxamine 5'-phosphate (PMP) as a substrate.1 Publication

Miscellaneous

The electron density for the FMN cofactor is weak in the crystal structure (PDB 2A2J), which does not allow FMN to be definitively placed in the M.tuberculosis PNPOx active site, but the residues known to interact with FMN in the E.coli and human PNPOx enzymes are found to be conserved.Curated

<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 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

FMNUniRule annotation1 PublicationNote: Appears to bind only one FMN molecule per homodimer.1 Publication

<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 0.01 sec(-1).1 Publication
  1. KM=360 µM for pyridoxine 5'-phosphate1 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: pyridoxal 5'-phosphate salvage

    This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate.UniRule annotation1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Pyridoxine 5'-phosphate oxidase (pdxH)
    This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxine 5'-phosphate, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

    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 sitei81SubstrateUniRule annotation1
    Binding sitei98FMNUniRule annotation1
    Binding sitei120FMNUniRule annotation1
    Binding sitei138SubstrateUniRule annotation1
    Binding sitei142SubstrateUniRule annotation1
    Binding sitei201FMNUniRule annotation1
    Binding sitei211FMNUniRule annotation1

    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 bindingi76 – 81FMNUniRule annotation6
    Nucleotide bindingi91 – 92FMNUniRule annotation2
    Nucleotide bindingi155 – 156FMNUniRule annotation2

    <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 functionOxidoreductase
    Biological processPyridoxine biosynthesis
    LigandFlavoprotein, FMN

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MTBH37RV:G185E-6850-MONOMER

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

    More...
    UniPathwayi
    UPA01068;UER00305

    <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 5'-phosphate oxidase1 Publication (EC:1.4.3.5UniRule annotation1 Publication)
    Short name:
    PNP oxidase1 Publication
    Short name:
    PNPOx1 Publication
    Alternative name(s):
    Pyridoxal 5'-phosphate synthaseUniRule annotation
    <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:pdxH1 Publication
    Ordered Locus Names:Rv2607
    ORF Names:MTCY1A10.26c
    <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>OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
    <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 identifieri83332 [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 lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
    <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
    • UP000001584 <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

    Organism-specific databases

    Mycobacterium tuberculosis strain H37Rv genome database

    More...
    TubercuListi
    Rv2607

    <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_00001677231 – 224Pyridoxine 5'-phosphate oxidaseAdd BLAST224

    Proteomic databases

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

    More...
    PaxDbi
    P9WIJ1

    <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.

    UniRule annotation2 Publications

    GO - Molecular functioni

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    83332.Rv2607

    <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

    Secondary structure

    1224
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

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

    More...
    SMRi
    P9WIJ1

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    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>Regioni19 – 22Substrate bindingUniRule annotation4
    Regioni207 – 209Substrate bindingUniRule annotation3

    <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 pyridoxamine 5'-phosphate oxidase family.UniRule annotation

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4108S7T Bacteria
    COG0259 LUCA

    KEGG Orthology (KO)

    More...
    KOi
    K00275

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    PEPNAMV

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P9WIJ1

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    2.30.110.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_01629 PdxH, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR000659 Pyridox_Oxase
    IPR019740 Pyridox_Oxase_CS
    IPR011576 Pyridox_Oxase_put
    IPR019576 Pyridoxamine_oxidase_dimer_C
    IPR012349 Split_barrel_FMN-bd

    The PANTHER Classification System

    More...
    PANTHERi
    PTHR10851 PTHR10851, 1 hit

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF10590 PNP_phzG_C, 1 hit
    PF01243 Putative_PNPOx, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF000190 Pyd_amn-ph_oxd, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00558 pdxH, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS01064 PYRIDOX_OXIDASE, 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.

    P9WIJ1-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MDDDAQMVAI DKDQLARMRG EYGPEKDGCG DLDFDWLDDG WLTLLRRWLN
    60 70 80 90 100
    DAQRAGVSEP NAMVLATVAD GKPVTRSVLC KILDESGVAF FTSYTSAKGE
    110 120 130 140 150
    QLAVTPYASA TFPWYQLGRQ AHVQGPVSKV STEEIFTYWS MRPRGAQLGA
    160 170 180 190 200
    WASQQSRPVG SRAQLDNQLA EVTRRFADQD QIPVPPGWGG YRIAPEIVEF
    210 220
    WQGRENRMHN RIRVANGRLE RLQP
    Length:224
    Mass (Da):25,186
    Last modified:April 16, 2014 - 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:i66ABC0AAACE90DC1
    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
    AL123456 Genomic DNA Translation: CCP45404.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    F70570

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_217123.1, NC_000962.3
    WP_003413471.1, NZ_NVQJ01000023.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CCP45404; CCP45404; Rv2607

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    888155

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    mtu:Rv2607
    mtv:RVBD_2607

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|83332.111.peg.2911

    <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
    AL123456 Genomic DNA Translation: CCP45404.1
    PIRiF70570
    RefSeqiNP_217123.1, NC_000962.3
    WP_003413471.1, NZ_NVQJ01000023.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2A2JX-ray2.50A/B1-224[»]
    SMRiP9WIJ1
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi83332.Rv2607

    Proteomic databases

    PaxDbiP9WIJ1

    Genome annotation databases

    EnsemblBacteriaiCCP45404; CCP45404; Rv2607
    GeneIDi888155
    KEGGimtu:Rv2607
    mtv:RVBD_2607
    PATRICifig|83332.111.peg.2911

    Organism-specific databases

    TubercuListiRv2607

    Phylogenomic databases

    eggNOGiENOG4108S7T Bacteria
    COG0259 LUCA
    KOiK00275
    OMAiPEPNAMV
    PhylomeDBiP9WIJ1

    Enzyme and pathway databases

    UniPathwayiUPA01068;UER00305
    BioCyciMTBH37RV:G185E-6850-MONOMER

    Family and domain databases

    Gene3Di2.30.110.10, 1 hit
    HAMAPiMF_01629 PdxH, 1 hit
    InterProiView protein in InterPro
    IPR000659 Pyridox_Oxase
    IPR019740 Pyridox_Oxase_CS
    IPR011576 Pyridox_Oxase_put
    IPR019576 Pyridoxamine_oxidase_dimer_C
    IPR012349 Split_barrel_FMN-bd
    PANTHERiPTHR10851 PTHR10851, 1 hit
    PfamiView protein in Pfam
    PF10590 PNP_phzG_C, 1 hit
    PF01243 Putative_PNPOx, 1 hit
    PIRSFiPIRSF000190 Pyd_amn-ph_oxd, 1 hit
    TIGRFAMsiTIGR00558 pdxH, 1 hit
    PROSITEiView protein in PROSITE
    PS01064 PYRIDOX_OXIDASE, 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 nameiPDXH_MYCTU
    <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: P9WIJ1
    Secondary accession number(s): L0TBR8, O06207, P65682
    <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: April 16, 2014
    Last sequence update: April 16, 2014
    Last modified: September 18, 2019
    This is version 30 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
      Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
    3. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    4. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
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