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Q88E47

- HGD_PSEPK

UniProt

Q88E47 - HGD_PSEPK

Protein

Homogentisate 1,2-dioxygenase

Gene

hmgA

Organism
Pseudomonas putida (strain KT2440)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 74 (01 Oct 2014)
      Sequence version 1 (06 Jun 2003)
      Previous versions | rss
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    Functioni

    Involved in the catabolism of homogentisate (2,5-dihydroxyphenylacetate or 2,5-OH-PhAc), a central intermediate in the degradation of phenylalanine and tyrosine. Catalyzes the oxidative ring cleavage of the ar omatic ring of 2,5-dihydroxyphenylacetate to yield maleylacetoacetate.2 Publications

    Catalytic activityi

    Homogentisate + O2 = 4-maleylacetoacetate.1 PublicationUniRule annotation

    Cofactori

    Iron.1 PublicationUniRule annotation

    Kineticsi

    Kcat is 79.5 sec(-1) for the oxidative ring cleavage of homogentisate.

    1. KM=53.2 µM for homogentisate2 Publications

    Vmax=99.4 µmol/min/mg enzyme2 Publications

    Temperature dependencei

    Optimum temperature is 37 degrees Celsius.2 Publications

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei288 – 2881Proton acceptor1 PublicationUniRule annotation
    Metal bindingi331 – 3311Iron
    Metal bindingi337 – 3371Iron
    Binding sitei346 – 3461homogentisate1 PublicationUniRule annotation
    Metal bindingi367 – 3671Iron
    Binding sitei367 – 3671homogentisate1 PublicationUniRule annotation

    GO - Molecular functioni

    1. homogentisate 1,2-dioxygenase activity Source: UniProtKB
    2. iron ion binding Source: UniProtKB

    GO - Biological processi

    1. L-phenylalanine catabolic process Source: UniProtKB
    2. tyrosine catabolic process Source: UniProtKB

    Keywords - Molecular functioni

    Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Phenylalanine catabolism, Tyrosine catabolism

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciPPUT160488:GIXO-4708-MONOMER.
    UniPathwayiUPA00139; UER00339.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Homogentisate 1,2-dioxygenaseUniRule annotation (EC:1.13.11.5UniRule annotation)
    Short name:
    HGDOUniRule annotation
    Alternative name(s):
    Homogentisate oxygenaseUniRule annotation
    Homogentisic acid oxidaseUniRule annotation
    HomogentisicaseUniRule annotation
    Gene namesi
    Name:hmgAUniRule annotation
    Ordered Locus Names:PP_4621
    OrganismiPseudomonas putida (strain KT2440)
    Taxonomic identifieri160488 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
    ProteomesiUP000000556: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi288 – 2881H → F: Reduces the catalytic efficiency 75-fold. 1 Publication
    Mutagenesisi346 – 3461Y → F: Decreases the affinity for homogentisate more than 60-fold and reduces the catalytic efficiency 20-fold. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 433433Homogentisate 1,2-dioxygenasePRO_0000220250Add
    BLAST

    Expressioni

    Inductioni

    Induced by homogentisate and repressed by HmgR.

    Interactioni

    Subunit structurei

    Hexamer; dimer of trimers.1 PublicationUniRule annotation

    Protein-protein interaction databases

    STRINGi160488.PP_4621.

    Structurei

    Secondary structure

    1
    433
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 133
    Beta strandi19 – 246
    Beta strandi35 – 373
    Helixi39 – 413
    Beta strandi43 – 486
    Helixi56 – 583
    Beta strandi61 – 688
    Beta strandi96 – 983
    Turni110 – 1123
    Beta strandi114 – 1218
    Beta strandi128 – 13811
    Beta strandi141 – 1488
    Beta strandi150 – 1589
    Beta strandi160 – 1645
    Beta strandi167 – 1715
    Beta strandi175 – 1795
    Beta strandi185 – 1895
    Beta strandi194 – 2018
    Helixi212 – 2143
    Helixi222 – 2243
    Beta strandi226 – 2283
    Beta strandi236 – 24510
    Beta strandi248 – 2569
    Beta strandi261 – 2677
    Beta strandi271 – 2744
    Helixi275 – 2773
    Beta strandi281 – 2877
    Helixi291 – 2944
    Beta strandi295 – 2995
    Beta strandi308 – 3147
    Beta strandi316 – 3194
    Beta strandi330 – 34415
    Beta strandi350 – 3523
    Beta strandi358 – 3614
    Helixi371 – 3799
    Beta strandi385 – 3873
    Beta strandi391 – 3999
    Beta strandi402 – 4043
    Helixi405 – 4095
    Helixi417 – 4215

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3ZDSX-ray1.70A/B/C/D/E/F/G/H/I/J/K/L1-433[»]
    4AQ2X-ray1.95A/B/C/D/E/F/G/H/I/J/K/L1-433[»]
    4AQ6X-ray1.98A/B/C/D/E/F/G/H/I/J/K/L1-433[»]
    ProteinModelPortaliQ88E47.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the homogentisate dioxygenase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG3508.
    HOGENOMiHOG000139824.
    KOiK00451.
    OMAiRCFYNSD.
    OrthoDBiEOG6D5FZK.

    Family and domain databases

    Gene3Di2.60.120.10. 2 hits.
    HAMAPiMF_00334. Homogentis_dioxygen.
    InterProiIPR005708. Homogentis_dOase.
    IPR022950. Homogentis_dOase_bac.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view]
    PANTHERiPTHR11056. PTHR11056. 1 hit.
    PfamiPF04209. HgmA. 1 hit.
    [Graphical view]
    SUPFAMiSSF51182. SSF51182. 1 hit.
    TIGRFAMsiTIGR01015. hmgA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q88E47-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNRDTSPDLH YLSGFGNEFA SEALPGALPV GQNSPQKAPY GLYAELLSGT    50
    AFTMARSELR RTWLYRIRPS ALHPRFERLA RQPLGGPLGG INPNRLRWSP 100
    QPIPAEPTDF IEGWLPMAAN AGAEKPAGVS IYIYRANRSM ERVFFNADGE 150
    LLLVPEQGRL RIATELGVME VEPLEIAVIP RGMKFRVELL DGQARGYIAE 200
    NHGAPLRLPD LGPIGSNGLA NPRDFLTPVA HYEEAEGPVQ LVQKFLGEHW 250
    ACELQHSPLD VVAWHGSNVP YKYDLRRFNT IGTVSFDHPD PSIFTVLTSP 300
    TSVHGMANMD FVIFPPRWMV AENTFRPPWF HRNLMNEFMG LINGAYDAKA 350
    EGFLPGGASL HGVMSAHGPD AETCEKAIAA DLAPHKIDNT MAFMFETSQV 400
    LRPSLQALEC PQLQADYDSC WATLPSTFNP NRR 433
    Length:433
    Mass (Da):48,011
    Last modified:June 6, 2003 - v1
    Checksum:i6D5F4C7F91BE4512
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE015451 Genomic DNA. Translation: AAN70194.1.
    RefSeqiNP_746730.1. NC_002947.3.
    WP_010955283.1. NC_002947.3.

    Genome annotation databases

    EnsemblBacteriaiAAN70194; AAN70194; PP_4621.
    GeneIDi1041590.
    KEGGippu:PP_4621.
    PATRICi19947980. VBIPsePut30601_4927.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE015451 Genomic DNA. Translation: AAN70194.1 .
    RefSeqi NP_746730.1. NC_002947.3.
    WP_010955283.1. NC_002947.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3ZDS X-ray 1.70 A/B/C/D/E/F/G/H/I/J/K/L 1-433 [» ]
    4AQ2 X-ray 1.95 A/B/C/D/E/F/G/H/I/J/K/L 1-433 [» ]
    4AQ6 X-ray 1.98 A/B/C/D/E/F/G/H/I/J/K/L 1-433 [» ]
    ProteinModelPortali Q88E47.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 160488.PP_4621.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAN70194 ; AAN70194 ; PP_4621 .
    GeneIDi 1041590.
    KEGGi ppu:PP_4621.
    PATRICi 19947980. VBIPsePut30601_4927.

    Phylogenomic databases

    eggNOGi COG3508.
    HOGENOMi HOG000139824.
    KOi K00451.
    OMAi RCFYNSD.
    OrthoDBi EOG6D5FZK.

    Enzyme and pathway databases

    UniPathwayi UPA00139 ; UER00339 .
    BioCyci PPUT160488:GIXO-4708-MONOMER.

    Family and domain databases

    Gene3Di 2.60.120.10. 2 hits.
    HAMAPi MF_00334. Homogentis_dioxygen.
    InterProi IPR005708. Homogentis_dOase.
    IPR022950. Homogentis_dOase_bac.
    IPR014710. RmlC-like_jellyroll.
    IPR011051. RmlC_Cupin.
    [Graphical view ]
    PANTHERi PTHR11056. PTHR11056. 1 hit.
    Pfami PF04209. HgmA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51182. SSF51182. 1 hit.
    TIGRFAMsi TIGR01015. hmgA. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: KT2440.
    2. "The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida."
      Arias-Barrau E., Olivera E.R., Luengo J.M., Fernandez C., Galan B., Garcia J.L., Diaz E., Minambres B.
      J. Bacteriol. 186:5062-5077(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: U.
    3. "Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase."
      Jeoung J.H., Bommer M., Lin T.Y., Dobbek H.
      Proc. Natl. Acad. Sci. U.S.A. 110:12625-12630(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH HOMOGENTISATE AND IRON IONS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF HIS-288 AND TYR-346, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, REACTION MECHANISM, SUBUNIT.

    Entry informationi

    Entry nameiHGD_PSEPK
    AccessioniPrimary (citable) accession number: Q88E47
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 6, 2003
    Last sequence update: June 6, 2003
    Last modified: October 1, 2014
    This is version 74 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, 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

    External Data

    Dasty 3