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Protein

2-hydroxychromene-2-carboxylate isomerase

Gene

nahD

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the naphthalene catabolic pathway. Catalyzes the reversible glutathione-dependent isomerization of 2-hydroxychromene-2-carboxylate (HCCA) to trans-O-hydroxybenzylidenepyruvate (THBPA).2 Publications

Catalytic activityi

2-hydroxy-2H-chromene-2-carboxylate = (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate.1 Publication

Cofactori

glutathione2 PublicationsNote: Glutathione seems to stabilize the enzyme, which loses activity rapidly in the absence of this compound.2 Publications

Kineticsi

Kcat is 47 sec(-1) for HCCA, 19 sec(-1) for THBPA and 39 sec(-1) for glutathion.

  1. KM=0.2 mM for HCCA (at pH 10)2 Publications
  2. KM=17 µM for glutathione (at pH 7 and 25 degrees Celsius)2 Publications
  3. KM=84 µM for HCCA (at pH 7 and 25 degrees Celsius)2 Publications
  4. KM=138 µM for THBPA (at pH 7 and 25 degrees Celsius)2 Publications

    pH dependencei

    Optimum pH is 10.2 Publications

    Pathwayi: naphthalene degradation

    This protein is involved in the pathway naphthalene degradation, which is part of Aromatic compound metabolism.
    View all proteins of this organism that are known to be involved in the pathway naphthalene degradation and in Aromatic compound metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei11Nucleophile1 Publication1
    Binding sitei11Glutathione1 Publication1
    Binding sitei43Substrate1 Publication1
    Binding sitei84Substrate1 Publication1
    Binding sitei168Glutathione; via amide nitrogen and carbonyl oxygen1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    • naphthalene catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-12808.
    BRENDAi5.99.1.4. 5092.
    UniPathwayiUPA00082.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    2-hydroxychromene-2-carboxylate isomerase (EC:5.99.1.4)
    Short name:
    HCCA isomerase
    Gene namesi
    Name:nahD
    Encoded oniPlasmid NAH70 Publication
    OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    Taxonomic identifieri303 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000967001 – 2032-hydroxychromene-2-carboxylate isomeraseAdd BLAST203

    Structurei

    Secondary structure

    1203
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 7Combined sources6
    Helixi12 – 28Combined sources17
    Beta strandi31 – 36Combined sources6
    Helixi39 – 46Combined sources8
    Helixi53 – 55Combined sources3
    Helixi57 – 74Combined sources18
    Helixi87 – 92Combined sources6
    Helixi93 – 95Combined sources3
    Helixi99 – 115Combined sources17
    Helixi125 – 133Combined sources9
    Helixi137 – 145Combined sources9
    Helixi147 – 162Combined sources16
    Beta strandi167 – 173Combined sources7
    Beta strandi176 – 180Combined sources5
    Helixi181 – 183Combined sources3
    Helixi184 – 198Combined sources15

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2IMDX-ray1.60A1-203[»]
    2IMEX-ray1.70A1-203[»]
    2IMFX-ray1.30A1-203[»]
    ProteinModelPortaliQ51948.
    SMRiQ51948.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ51948.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni53 – 54Substrate binding2
    Regioni179 – 182Glutathione binding4

    Sequence similaritiesi

    Belongs to the GST superfamily. NadH family.Curated

    Phylogenomic databases

    KOiK14584.

    Family and domain databases

    Gene3Di3.40.30.10. 1 hit.
    InterProiIPR001853. DSBA-like_thioredoxin_dom.
    IPR014440. HCCAis_GSTk.
    IPR012336. Thioredoxin-like_fold.
    [Graphical view]
    PfamiPF01323. DSBA. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006386. HCCAis_GSTk. 1 hit.
    SUPFAMiSSF52833. SSF52833. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q51948-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIVDFYFDFL SPFSYLANQR LSKLAQDYGL TIRYNAIDLA RVKIAIGNVG
    60 70 80 90 100
    PSNRDLKVKL DYLKVDLQRW AQLYGIPLVF PANYNSRRMN IGFYYSGAEA
    110 120 130 140 150
    QAAAYVNVVF NAVWGEGIAP DLESLPALVS EKLGWDRSAF EHFLSSNAAT
    160 170 180 190 200
    ERYDEQTHAA IERKVFGVPT MFLGDEMWWG NDRLFMLESA MGRLCRQNAD

    LSS
    Length:203
    Mass (Da):23,061
    Last modified:November 1, 1996 - v1
    Checksum:iE84B56F21C604945
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U09057 Genomic DNA. Translation: AAA66358.1.
    PIRiC55552.
    RefSeqiWP_011475384.1. NC_007926.1.
    YP_534829.1. NC_007926.1.

    Genome annotation databases

    GeneIDi3974213.
    KEGGiag:AAA66358.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U09057 Genomic DNA. Translation: AAA66358.1.
    PIRiC55552.
    RefSeqiWP_011475384.1. NC_007926.1.
    YP_534829.1. NC_007926.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2IMDX-ray1.60A1-203[»]
    2IMEX-ray1.70A1-203[»]
    2IMFX-ray1.30A1-203[»]
    ProteinModelPortaliQ51948.
    SMRiQ51948.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    GeneIDi3974213.
    KEGGiag:AAA66358.

    Phylogenomic databases

    KOiK14584.

    Enzyme and pathway databases

    UniPathwayiUPA00082.
    BioCyciMetaCyc:MONOMER-12808.
    BRENDAi5.99.1.4. 5092.

    Miscellaneous databases

    EvolutionaryTraceiQ51948.
    PROiQ51948.

    Family and domain databases

    Gene3Di3.40.30.10. 1 hit.
    InterProiIPR001853. DSBA-like_thioredoxin_dom.
    IPR014440. HCCAis_GSTk.
    IPR012336. Thioredoxin-like_fold.
    [Graphical view]
    PfamiPF01323. DSBA. 1 hit.
    [Graphical view]
    PIRSFiPIRSF006386. HCCAis_GSTk. 1 hit.
    SUPFAMiSSF52833. SSF52833. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNAHD_PSEPU
    AccessioniPrimary (citable) accession number: Q51948
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 1996
    Last modified: November 30, 2016
    This is version 89 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, Plasmid

    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.