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Entry version 96 (17 Jun 2020)
Sequence version 1 (01 Jun 2001)
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Protein

D-xylonate dehydratase

Gene

xylD

Organism
Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus)
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 dehydration of D-xylonate to 2-dehydro-3-deoxy-D-arabinonate during D-xylose degradation. Can also dehydrate D-gluconate, with similar catalytic efficiency. Has weak activity with D-galactonate, D-fuconate and L-arabinonate.1 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 '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:

<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 1406 min(-1) with D-xylonate as substrate. kcat is 2626 min(-1) with D-gluconate as substrate. kcat is 46 min(-1) with L-arabinonate as substrate. kcat is 218 min(-1) with D-galactonate as substrate. kcat is 196 min(-1) with D-fuconate as substrate.1 Publication
  1. KM=1.9 mM for D-xylonate1 Publication
  2. KM=4.0 mM for D-gluconate1 Publication
  3. KM=7.8 mM for L-arabinonate1 Publication
  4. KM=5.2 mM for D-galactonate1 Publication
  5. KM=5.8 mM for D-fuconate1 Publication

    pH dependencei

    Optimum pH is 8.5.1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: D-xylose degradation

    This protein is involved in the pathway D-xylose degradation, which is part of Carbohydrate metabolism.1 Publication
    View all proteins of this organism that are known to be involved in the pathway D-xylose degradation and in Carbohydrate metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <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 bindingi64Iron-sulfur (2Fe-2S)1 Publication1
    Metal bindingi96Magnesium1 Publication1
    Metal bindingi132Iron-sulfur (2Fe-2S)1 Publication1
    Metal bindingi133Magnesium1 Publication1
    Metal bindingi205Iron-sulfur (2Fe-2S)1 Publication1
    Metal bindingi467Magnesium1 Publication1

    <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 functionLyase
    Biological processCarbohydrate metabolism, Xylose metabolism
    Ligand2Fe-2S, Iron, Iron-sulfur, Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    CAULO:CC0819-MONOMER

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

    More...
    UniPathwayi
    UPA00810

    <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 dehydratase1 Publication (EC:4.2.1.821 Publication)
    Short name:
    XyDHT1 Publication
    Alternative name(s):
    Gluconate dehydrataseCurated (EC:4.2.1.391 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:xylD1 Publication
    Ordered Locus Names:CC_0819Imported
    <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>OrganismiCaulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus)
    <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 identifieri190650 [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 lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaeCaulobacter
    <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
    • UP000001816 <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

    <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

    Deletion mutant cannot grow with D-xylose as the sole carbon source.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi64C → S: Strong decrease in activity. Does not bind iron-sulfur cluster. 1 Publication1
    Mutagenesisi132C → S: Almost loss of activity. Does not bind iron-sulfur cluster. 1 Publication1
    Mutagenesisi205C → S: Strong decrease in activity. Does not bind iron-sulfur cluster. 1 Publication1
    Mutagenesisi450C → S: Slight decrease in activity. Does not affect binding of iron-sulfur cluster. 1 Publication1

    <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_00004488001 – 595D-xylonate dehydrataseAdd BLAST595

    <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.

    2 Publications

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    190650.CC_0819

    <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

    1595
    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
    Q9A9Z2

    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

    <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
    ENOG4105C01 Bacteria
    COG0129 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_014271_3_1_5

    KEGG Orthology (KO)

    More...
    KOi
    K22186

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    FDFAIMK

    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
    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

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00886 ILVD_EDD_1, 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.

    Q9A9Z2-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MRSALSNRTP RRFRSRDWFD NPDHIDMTAL YLERFMNYGI TPEELRSGKP
    60 70 80 90 100
    IIGIAQTGSD ISPCNRIHLD LVQRVRDGIR DAGGIPMEFP VHPIFENCRR
    110 120 130 140 150
    PTAALDRNLS YLGLVETLHG YPIDAVVLTT GCDKTTPAGI MAATTVNIPA
    160 170 180 190 200
    IVLSGGPMLD GWHENELVGS GTVIWRSRRK LAAGEITEEE FIDRAASSAP
    210 220 230 240 250
    SAGHCNTMGT ASTMNAVAEA LGLSLTGCAA IPAPYRERGQ MAYKTGQRIV
    260 270 280 290 300
    DLAYDDVKPL DILTKQAFEN AIALVAAAGG STNAQPHIVA MARHAGVEIT
    310 320 330 340 350
    ADDWRAAYDI PLIVNMQPAG KYLGERFHRA GGAPAVLWEL LQQGRLHGDV
    360 370 380 390 400
    LTVTGKTMSE NLQGRETSDR EVIFPYHEPL AEKAGFLVLK GNLFDFAIMK
    410 420 430 440 450
    SSVIGEEFRK RYLSQPGQEG VFEARAIVFD GSDDYHKRIN DPALEIDERC
    460 470 480 490 500
    ILVIRGAGPI GWPGSAEVVN MQPPDHLLKK GIMSLPTLGD GRQSGTADSP
    510 520 530 540 550
    SILNASPESA IGGGLSWLRT GDTIRIDLNT GRCDALVDEA TIAARKQDGI
    560 570 580 590
    PAVPATMTPW QEIYRAHASQ LDTGGVLEFA VKYQDLAAKL PRHNH
    Length:595
    Mass (Da):64,626
    Last modified:June 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:iC0F329411CBB089D
    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
    AE005673 Genomic DNA Translation: AAK22804.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    H87350

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_419636.1, NC_002696.2
    WP_010918704.1, NC_002696.2

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAK22804; AAK22804; CC_0819

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    942636

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ccr:CC_0819

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|190650.5.peg.832

    <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
    AE005673 Genomic DNA Translation: AAK22804.1
    PIRiH87350
    RefSeqiNP_419636.1, NC_002696.2
    WP_010918704.1, NC_002696.2

    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
    5OYNX-ray2.70A/B/C/D6-595[»]
    SMRiQ9A9Z2
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi190650.CC_0819

    Genome annotation databases

    EnsemblBacteriaiAAK22804; AAK22804; CC_0819
    GeneIDi942636
    KEGGiccr:CC_0819
    PATRICifig|190650.5.peg.832

    Phylogenomic databases

    eggNOGiENOG4105C01 Bacteria
    COG0129 LUCA
    HOGENOMiCLU_014271_3_1_5
    KOiK22186
    OMAiFDFAIMK

    Enzyme and pathway databases

    UniPathwayiUPA00810
    BioCyciCAULO:CC0819-MONOMER

    Family and domain databases

    Gene3Di3.50.30.80, 1 hit
    InterProiView protein in InterPro
    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
    PROSITEiView protein in PROSITE
    PS00886 ILVD_EDD_1, 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 nameiXYLD_CAUVC
    <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: Q9A9Z2
    <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: December 11, 2019
    Last sequence update: June 1, 2001
    Last modified: June 17, 2020
    This is version 96 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, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
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