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Protein

1,4-dihydroxy-2-naphthoyl-CoA hydrolase

Gene

menI

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA). Also shows significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB.3 Publications

Catalytic activityi

1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA.UniRule annotation2 Publications

Kineticsi

kcat is 6.2 sec(-1) with 1,4-dihydroxy-2-naphthoyl-CoA (PubMed:23564174). kcat is 1.6 sec(-1) with 1,4-dihydroxy-2-naphthoyl-CoA (PubMed:24992697). kcat is 0.12 sec(-1) with oleoyl-CoA. kcat is 0.62 sec(-1) with myristoyl-CoA. kcat is 0.0044 sec(-1) with acetyl-CoA. kcat is 0.58 sec(-1) with palmitoyl-CoA. kcat is 0.74 sec(-1) with lauroyl-CoA. kcat is 14.8 sec(-1) with 1-hydroxy-2-naphthoyl-CoA. kcat is 5.2 sec(-1) with 4-hydroxybenzoyl-CoA. kcat is 0.3 sec(-1) with hexanoyl-CoA. kcat is 17.7 sec(-1) with benzoyl-CoA. kcat is 12.6 sec(-1) with 3,5-dihydroxybenzoyl-CoA. kcat is 23.2 sec(-1) with 3,4-dihydroxybenzoyl-CoA. kcat is 8.4 sec(-1) with coumaroyl-CoA. kcat is 0.083 sec(-1) with benzoyl-ACP. kcat is 0.5 sec(-1) with beta-methylcrotonyl-CoA. kcat is 93.0 sec(-1) with salicylyl-CoA. kcat is 0.67 sec(-1) with beta-methylmalonyl-CoA. kcat is 0.21 sec(-1) with propionyl-CoA. kcat is 0.0036 sec(-1) with 2,4-dihydroxybenzoyl-EntB.2 Publications

  1. KM=2.5 µM for 1,4-dihydroxy-2-naphthoyl-CoA1 Publication
  2. KM=8 µM for 1,4-dihydroxy-2-naphthoyl-CoA1 Publication
  3. KM=1.3 µM for oleoyl-CoA1 Publication
  4. KM=1.5 µM for myristoyl-CoA1 Publication
  5. KM=1.559 µM for acetyl-CoA1 Publication
  6. KM=1.9 µM for palmitoyl-CoA1 Publication
  7. KM=2.2 µM for lauroyl-CoA1 Publication
  8. KM=8.0 µM for 1-hydroxy-2-naphthoyl-CoA1 Publication
  9. KM=9 µM for 4-hydroxybenzoyl-CoA1 Publication
  10. KM=21 µM for hexanoyl-CoA1 Publication
  11. KM=25 µM for benzoyl-CoA1 Publication
  12. KM=26.5 µM for 3,5-dihydroxybenzoyl-CoA1 Publication
  13. KM=26.9 µM for 3,4-dihydroxybenzoyl-CoA1 Publication
  14. KM=30 µM for coumaroyl-CoA1 Publication
  15. KM=54 µM for benzoyl-ACP1 Publication
  16. KM=69.4 µM for beta-methylcrotonyl-CoA1 Publication
  17. KM=73 µM for salicylyl-CoA1 Publication
  18. KM=115 µM for beta-methylmalonyl-CoA1 Publication
  19. KM=120 µM for propionyl-CoA1 Publication
  20. KM=200 µM for 2,4-dihydroxybenzoyl-EntB1 Publication

    Pathwayi: 1,4-dihydroxy-2-naphthoate biosynthesis

    This protein is involved in step 7 of the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate.UniRule annotation2 Publications
    Proteins known to be involved in the 7 steps of the subpathway in this organism are:
    1. Isochorismate synthase MenF (menF)
    2. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase (menD)
    3. 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (menH)
    4. o-succinylbenzoate synthase (menC)
    5. 2-succinylbenzoate--CoA ligase (menE)
    6. 1,4-dihydroxy-2-naphthoyl-CoA synthase (menB)
    7. 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (menI)
    This subpathway is part of the pathway 1,4-dihydroxy-2-naphthoate biosynthesis, which is itself part of Quinol/quinone metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate, the pathway 1,4-dihydroxy-2-naphthoate biosynthesis and in Quinol/quinone metabolism.

    Pathwayi: menaquinone biosynthesis

    This protein is involved in the pathway menaquinone biosynthesis, which is part of Quinol/quinone metabolism.UniRule annotation2 Publications
    View all proteins of this organism that are known to be involved in the pathway menaquinone biosynthesis and in Quinol/quinone metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei63 – 631Nucleophile or proton acceptor1 PublicationUniRule annotation
    Binding sitei82 – 821Substrate; via carbonyl oxygenUniRule annotation1 Publication

    GO - Molecular functioni

    • 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity Source: EcoCyc
    • CoA hydrolase activity Source: EcoCyc
    • hydrolase activity Source: EcoCyc

    GO - Biological processi

    • menaquinone biosynthetic process Source: CACAO
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Menaquinone biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:G6912-MONOMER.
    ECOL316407:JW1676-MONOMER.
    MetaCyc:G6912-MONOMER.
    BRENDAi3.1.2.2. 2026.
    UniPathwayiUPA00079.
    UPA01057; UER01033.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    1,4-dihydroxy-2-naphthoyl-CoA hydrolaseUniRule annotationCurated (EC:3.1.2.28UniRule annotation2 Publications)
    Short name:
    DHNA-CoA hydrolaseUniRule annotationCurated
    Alternative name(s):
    DHNA-CoA thioesterase1 PublicationUniRule annotation
    Gene namesi
    Name:menI1 PublicationUniRule annotation
    Synonyms:ydiI
    Ordered Locus Names:b1686, JW1676
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13968. menI.

    Pathology & Biotechi

    Disruption phenotypei

    Deletion results in a significant decrease in menaquinone production.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi48 – 481Q → A: Almost loss of activity with benzoyl-CoA as substrate. 1 Publication
    Mutagenesisi48 – 481Q → N: 51-fold decrease in catalytic efficiency toward benzoyl-CoA. 1 Publication
    Mutagenesisi54 – 541H → A: 514-fold decrease in catalytic efficiency toward benzoyl-CoA. 1 Publication
    Mutagenesisi54 – 541H → F: Almost loss of activity with benzoyl-CoA as substrate. 1 Publication
    Mutagenesisi63 – 631E → A or Q: Loss of activity with benzoyl-CoA as substrate. 1 Publication
    Mutagenesisi63 – 631E → D: Almost loss of activity with benzoyl-CoA as substrate. 1 Publication
    Mutagenesisi64 – 641S → A: Almost no change in catalytic efficiency toward benzoyl-CoA. 1 Publication
    Mutagenesisi67 – 671S → A: Almost no change in catalytic efficiency toward benzoyl-CoA. 1 Publication
    Mutagenesisi68 – 681V → M: 10-fold decrease in catalytic efficiency toward lauroyl-CoA. Does not affect catalytic efficiency toward 1,4-dihydroxy-2-naphthoyl-CoA and benzoyl-CoA. 1 Publication
    Mutagenesisi71 – 711Y → A: Does not affect activity. 1 Publication
    Mutagenesisi89 – 891H → A: 156-fold decrease in catalytic efficiency toward benzoyl-CoA. 1 Publication
    Mutagenesisi91 – 911R → A: 9-fold decrease in catalytic efficiency toward benzoyl-CoA. 1 Publication
    Mutagenesisi106 – 1061H → A: Almost no change in catalytic efficiency toward benzoyl-CoA. 1 Publication
    Mutagenesisi109 – 1091S → A: Almost no change in catalytic efficiency toward benzoyl-CoA. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 1361361,4-dihydroxy-2-naphthoyl-CoA hydrolasePRO_0000156678Add
    BLAST

    Proteomic databases

    PaxDbiP77781.
    PRIDEiP77781.

    Interactioni

    Subunit structurei

    Homotetramer. Dimer of dimers.UniRule annotation1 Publication

    Protein-protein interaction databases

    BioGridi4259131. 5 interactions.
    DIPiDIP-11750N.
    IntActiP77781. 2 interactions.
    STRINGi511145.b1686.

    Structurei

    Secondary structure

    1
    136
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 146Combined sources
    Turni15 – 184Combined sources
    Helixi20 – 234Combined sources
    Beta strandi27 – 315Combined sources
    Beta strandi36 – 416Combined sources
    Turni44 – 463Combined sources
    Beta strandi51 – 533Combined sources
    Helixi55 – 7218Combined sources
    Beta strandi79 – 8911Combined sources
    Beta strandi95 – 10713Combined sources
    Beta strandi109 – 11911Combined sources
    Beta strandi125 – 13612Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SBKX-ray2.00A/B/C/D1-136[»]
    1VH5X-ray1.34A/B2-136[»]
    1VI8X-ray2.20A/B/C/D/E/F/G/H2-136[»]
    4K49X-ray1.89A/B/C/D1-136[»]
    4K4AX-ray1.89A/B/C/D1-136[»]
    4K4BX-ray1.90A/B/C/D/E/F/G/H1-136[»]
    ProteinModelPortaliP77781.
    SMRiP77781. Positions 1-136.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77781.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni89 – 924Substrate bindingUniRule annotation1 Publication
    Regioni106 – 1116Substrate bindingUniRule annotation1 Publication

    Sequence similaritiesi

    Belongs to the thioesterase PaaI family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105KA0. Bacteria.
    COG2050. LUCA.
    HOGENOMiHOG000066991.
    InParanoidiP77781.
    KOiK19222.
    OMAiTQVWQID.
    OrthoDBiEOG6PGKBS.
    PhylomeDBiP77781.

    Family and domain databases

    Gene3Di3.10.129.10. 1 hit.
    HAMAPiMF_01936. MenI.
    InterProiIPR029069. HotDog_dom.
    IPR030863. MenI.
    IPR003736. PAAI_dom.
    IPR006683. Thioestr_dom.
    [Graphical view]
    PfamiPF03061. 4HBT. 1 hit.
    [Graphical view]
    SUPFAMiSSF54637. SSF54637. 1 hit.
    TIGRFAMsiTIGR00369. unchar_dom_1. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P77781-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIWKRKITLE ALNAMGEGNM VGFLDIRFEH IGDDTLEATM PVDSRTKQPF
    60 70 80 90 100
    GLLHGGASVV LAESIGSVAG YLCTEGEQKV VGLEINANHV RSAREGRVRG
    110 120 130
    VCKPLHLGSR HQVWQIEIFD EKGRLCCSSR LTTAIL
    Length:136
    Mass (Da):14,945
    Last modified:February 1, 1997 - v1
    Checksum:iE7B995390E7244C3
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74756.1.
    AP009048 Genomic DNA. Translation: BAA15452.1.
    PIRiF64926.
    RefSeqiNP_416201.1. NC_000913.3.
    WP_000637982.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74756; AAC74756; b1686.
    BAA15452; BAA15452; BAA15452.
    GeneIDi946190.
    KEGGiecj:JW1676.
    eco:b1686.
    PATRICi32118678. VBIEscCol129921_1757.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74756.1.
    AP009048 Genomic DNA. Translation: BAA15452.1.
    PIRiF64926.
    RefSeqiNP_416201.1. NC_000913.3.
    WP_000637982.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SBKX-ray2.00A/B/C/D1-136[»]
    1VH5X-ray1.34A/B2-136[»]
    1VI8X-ray2.20A/B/C/D/E/F/G/H2-136[»]
    4K49X-ray1.89A/B/C/D1-136[»]
    4K4AX-ray1.89A/B/C/D1-136[»]
    4K4BX-ray1.90A/B/C/D/E/F/G/H1-136[»]
    ProteinModelPortaliP77781.
    SMRiP77781. Positions 1-136.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259131. 5 interactions.
    DIPiDIP-11750N.
    IntActiP77781. 2 interactions.
    STRINGi511145.b1686.

    Proteomic databases

    PaxDbiP77781.
    PRIDEiP77781.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74756; AAC74756; b1686.
    BAA15452; BAA15452; BAA15452.
    GeneIDi946190.
    KEGGiecj:JW1676.
    eco:b1686.
    PATRICi32118678. VBIEscCol129921_1757.

    Organism-specific databases

    EchoBASEiEB3725.
    EcoGeneiEG13968. menI.

    Phylogenomic databases

    eggNOGiENOG4105KA0. Bacteria.
    COG2050. LUCA.
    HOGENOMiHOG000066991.
    InParanoidiP77781.
    KOiK19222.
    OMAiTQVWQID.
    OrthoDBiEOG6PGKBS.
    PhylomeDBiP77781.

    Enzyme and pathway databases

    UniPathwayiUPA00079.
    UPA01057; UER01033.
    BioCyciEcoCyc:G6912-MONOMER.
    ECOL316407:JW1676-MONOMER.
    MetaCyc:G6912-MONOMER.
    BRENDAi3.1.2.2. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP77781.
    PROiP77781.

    Family and domain databases

    Gene3Di3.10.129.10. 1 hit.
    HAMAPiMF_01936. MenI.
    InterProiIPR029069. HotDog_dom.
    IPR030863. MenI.
    IPR003736. PAAI_dom.
    IPR006683. Thioestr_dom.
    [Graphical view]
    PfamiPF03061. 4HBT. 1 hit.
    [Graphical view]
    SUPFAMiSSF54637. SSF54637. 1 hit.
    TIGRFAMsiTIGR00369. unchar_dom_1. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
      Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
      , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
      DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "Enzyme genomics: application of general enzymatic screens to discover new enzymes."
      Kuznetsova E., Proudfoot M., Sanders S.A., Reinking J., Savchenko A., Arrowsmith C.H., Edwards A.M., Yakunin A.F.
      FEMS Microbiol. Rev. 29:263-279(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS AN ESTERASE.
    5. "Identification of a hotdog fold thioesterase involved in the biosynthesis of menaquinone in Escherichia coli."
      Chen M., Ma X., Chen X., Jiang M., Song H., Guo Z.
      J. Bacteriol. 195:2768-2775(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, DISRUPTION PHENOTYPE.
      Strain: K12 / BW25113.
    6. "Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB."
      Latham J.A., Chen D., Allen K.N., Dunaway-Mariano D.
      Biochemistry 53:4775-4787(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, MUTAGENESIS OF VAL-68 AND TYR-71.
    7. "X-ray structure of YDII_ECOLI."
      Kuzin A.P., Edstrom W., Vorobiev S.M., Lee I., Forouhar F., Ma L., Chiang Y., Rong X., Acton T.B., Montelione G.T., Hunt J.F., Tong L.
      Submitted (FEB-2004) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
    8. Cited for: X-RAY CRYSTALLOGRAPHY (1.34 ANGSTROMS) OF 2-136.
    9. "Structure and catalysis in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB."
      Wu R., Latham J.A., Chen D., Farelli J., Zhao H., Matthews K., Allen K.N., Dunaway-Mariano D.
      Biochemistry 53:4788-4805(2014) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.89 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE ANALOGS, SUBUNIT, MUTAGENESIS OF GLN-48; HIS-54; GLU-63; SER-64; SER-67; HIS-89; ARG-91; HIS-106 AND SER-109, ACTIVE SITE.

    Entry informationi

    Entry nameiMENI_ECOLI
    AccessioniPrimary (citable) accession number: P77781
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 27, 2001
    Last sequence update: February 1, 1997
    Last modified: March 16, 2016
    This is version 126 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.