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Entry version 145 (10 Feb 2021)
Sequence version 2 (15 Jul 1998)
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Protein

D-xylonate dehydratase YjhG

Gene

yjhG

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 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 dehydration of D-xylonic acid to form 2-dehydro-3-deoxy-D-pentonate.1 Publication1 Publication

<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 <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Activity is increased in the presence of Mn+ and Mg2+. Inhibited by thiol compounds.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 0.33 min(-1).1 Publication
  1. KM=4.88 mM for D-xylonate1 Publication

    pH dependencei

    Optimum pH is 8.0.1 Publication

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.1 Publication

    <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

    • hydro-lyase activity Source: GO_Central
    • xylonate dehydratase activity Source: EcoCyc

    GO - Biological processi

    • aldonic acid catabolic process Source: EcoCyc

    <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 functionLyase

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    EcoCyc:G7910-MONOMER
    MetaCyc:G7910-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%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:
    D-xylonate dehydratase YjhG1 Publication (EC:4.2.1.821 Publication1 Publication)
    <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:yjhG
    Ordered Locus Names:b4297, JW4259
    <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>OrganismiEscherichia coli (strain K12)
    <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 identifieri83333 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    <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
    • UP000000318 <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
    • 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 provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    <p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Disruption mutant has reduced ability to catabolize D-xylonic acid. YjhG-yagF double mutant cannot use D-xylonate as the sole source of carbon.1 Publication

    <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_00001035611 – 655D-xylonate dehydratase YjhGAdd BLAST655

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...
    jPOSTi
    P39358

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

    More...
    PaxDbi
    P39358

    PRoteomics IDEntifications database

    More...
    PRIDEi
    P39358

    <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
    4260973, 10 interactors
    851170, 1 interactor

    Protein interaction database and analysis system

    More...
    IntActi
    P39358, 4 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    511145.b4297

    <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
    P39358

    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

    Belongs to the IlvD/Edd family.Curated

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG0129, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_014271_5_0_6

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    P39358

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.50.30.80, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR017798, Dehydratase_YjhG/YagF
    IPR042096, Dihydro-acid_dehy_C
    IPR000581, DiOHA_6PGluconate_deHydtase
    IPR020558, DiOHA_6PGluconate_deHydtase_CS
    IPR037237, IlvD/EDD_N

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00920, ILVD_EDD, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF143975, SSF143975, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR03432, yjhG_yagF, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00886, ILVD_EDD_1, 1 hit
    PS00887, ILVD_EDD_2, 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%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.

    P39358-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MSVRNIFADE SHDIYTVRTH ADGPDGELPL TAEMLINRPS GDLFGMTMNA
    60 70 80 90 100
    GMGWSPDELD RDGILLLSTL GGLRGADGKP VALALHQGHY ELDIQMKAAA
    110 120 130 140 150
    EVIKANHALP YAVYVSDPCD GRTQGTTGMF DSLPYRNDAS MVMRRLIRSL
    160 170 180 190 200
    PDAKAVIGVA SCDKGLPATM MALAAQHNIA TVLVPGGATL PAKDGEDNGK
    210 220 230 240 250
    VQTIGARFAN GELSLQDARR AGCKACASSG GGCQFLGTAG TSQVVAEGLG
    260 270 280 290 300
    LAIPHSALAP SGEPVWREIA RASARAALNL SQKGITTREI LTDKAIENAM
    310 320 330 340 350
    TVHAAFGGST NLLLHIPAIA HQAGCHIPTV DDWIRINKRV PRLVSVLPNG
    360 370 380 390 400
    PVYHPTVNAF MAGGVPEVML HLRSLGLLHE DVMTVTGSTL KENLDWWEHS
    410 420 430 440 450
    ERRQRFKQLL LDQEQINADE VIMSPQQAKA RGLTSTITFP VGNIAPEGSV
    460 470 480 490 500
    IKSTAIDPSM IDEQGIYYHK GVAKVYLSEK SAIYDIKHDK IKAGDILVII
    510 520 530 540 550
    GVGPSGTGME ETYQVTSALK HLSYGKHVSL ITDARFSGVS TGACIGHVGP
    560 570 580 590 600
    EALAGGPIGK LRTGDLIEIK IDCRELHGEV NFLGTRSDEQ LPSQEEATAI
    610 620 630 640 650
    LNARPSHQDL LPDPELPDDT RLWAMLQAVS GGTWTGCIYD VNKIGAALRD

    FMNKN
    Length:655
    Mass (Da):70,017
    Last modified:July 15, 1998 - 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:i95F88200CB6EF14C
    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 conflicti555 – 556GG → EA in AAA97193 (PubMed:7610040).Curated2

    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
    U14003 Genomic DNA Translation: AAA97193.1
    U00096 Genomic DNA Translation: AAC77253.1
    AP009048 Genomic DNA Translation: BAE78288.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    C65243

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_418717.1, NC_000913.3
    WP_000116326.1, NZ_SSUV01000012.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAC77253; AAC77253; b4297
    BAE78288; BAE78288; BAE78288

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    57730636
    946829

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ecj:JW4259
    eco:b4297

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|1411691.4.peg.2400

    <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
    U14003 Genomic DNA Translation: AAA97193.1
    U00096 Genomic DNA Translation: AAC77253.1
    AP009048 Genomic DNA Translation: BAE78288.1
    PIRiC65243
    RefSeqiNP_418717.1, NC_000913.3
    WP_000116326.1, NZ_SSUV01000012.1

    3D structure databases

    SMRiP39358
    ModBaseiSearch...

    Protein-protein interaction databases

    BioGRIDi4260973, 10 interactors
    851170, 1 interactor
    IntActiP39358, 4 interactors
    STRINGi511145.b4297

    Proteomic databases

    jPOSTiP39358
    PaxDbiP39358
    PRIDEiP39358

    Genome annotation databases

    EnsemblBacteriaiAAC77253; AAC77253; b4297
    BAE78288; BAE78288; BAE78288
    GeneIDi57730636
    946829
    KEGGiecj:JW4259
    eco:b4297
    PATRICifig|1411691.4.peg.2400

    Organism-specific databases

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

    More...
    EchoBASEi
    EB2437

    Phylogenomic databases

    eggNOGiCOG0129, Bacteria
    HOGENOMiCLU_014271_5_0_6
    PhylomeDBiP39358

    Enzyme and pathway databases

    BioCyciEcoCyc:G7910-MONOMER
    MetaCyc:G7910-MONOMER

    Miscellaneous databases

    Protein Ontology

    More...
    PROi
    PR:P39358

    Family and domain databases

    Gene3Di3.50.30.80, 1 hit
    InterProiView protein in InterPro
    IPR017798, Dehydratase_YjhG/YagF
    IPR042096, Dihydro-acid_dehy_C
    IPR000581, DiOHA_6PGluconate_deHydtase
    IPR020558, DiOHA_6PGluconate_deHydtase_CS
    IPR037237, IlvD/EDD_N
    PfamiView protein in Pfam
    PF00920, ILVD_EDD, 1 hit
    SUPFAMiSSF143975, SSF143975, 1 hit
    TIGRFAMsiTIGR03432, yjhG_yagF, 1 hit
    PROSITEiView protein in PROSITE
    PS00886, ILVD_EDD_1, 1 hit
    PS00887, ILVD_EDD_2, 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 nameiYJHG_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: P39358
    Secondary accession number(s): Q2M618
    <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: February 1, 1995
    Last sequence update: July 15, 1998
    Last modified: February 10, 2021
    This is version 145 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 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

    Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
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