Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

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

Gene

menB

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

Functioni

Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA).UniRule annotation4 Publications

Catalytic activityi

4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O.UniRule annotation4 Publications

Cofactori

bicarbonate1 Publication1 PublicationNote: The bicarbonate anion plays the same catalytic role (proton acceptor) as the side-chain carboxylate group of the essential 'Asp-185' found in actinobacteria, archaea, bacteroidetes, and deltaproteobacteria.1 Publication1 Publication

Enzyme regulationi

Inhibited by sulfite and nitrate.1 Publication

Kineticsi

kcat is 620 sec(-1) with o-succinylbenzoyl-CoA as substrate(PubMed:21830810). kcat is 1.24 min(-1) with o-succinylbenzoyl-CoA as substrate (PubMed:23658663). All assays are performed at pH 7.0 at 25 degrees Celsius and in the presence of 20 mM NaHCO3.2 Publications

  1. KM=26 µM for o-succinylbenzoyl-CoA1 Publication
  2. KM=2.8 µM for o-succinylbenzoyl-CoA1 Publication

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

    This protein is involved in step 6 of the subpathway that synthesizes 1,4-dihydroxy-2-naphthoate from chorismate.UniRule annotation
    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 annotation
    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
    Binding sitei45 – 451SubstrateUniRule annotation2 Publications
    Binding sitei97 – 971SubstrateUniRule annotation1 Publication
    Sitei97 – 971Important for catalysisUniRule annotation1 Publication
    Binding sitei155 – 1551SubstrateUniRule annotation2 Publications
    Binding sitei161 – 1611SubstrateUniRule annotation1 Publication
    Binding sitei258 – 2581Substrate; shared with neighboring subunitUniRule annotation1 Publication
    Sitei258 – 2581Important for catalysisUniRule annotation1 Publication
    Binding sitei273 – 2731Substrate; shared with neighboring subunitUniRule annotation2 Publications

    GO - Molecular functioni

    • 1,4-dihydroxy-2-naphthoyl-CoA synthase activity Source: EcoliWiki
    • bicarbonate binding Source: UniProtKB

    GO - Biological processi

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

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Menaquinone biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:NAPHTHOATE-SYN-MONOMER.
    ECOL316407:JW2257-MONOMER.
    MetaCyc:NAPHTHOATE-SYN-MONOMER.
    UniPathwayiUPA00079.
    UPA01057; UER00167.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    1,4-dihydroxy-2-naphthoyl-CoA synthase1 PublicationUniRule annotation (EC:4.1.3.36UniRule annotation4 Publications)
    Short name:
    DHNA-CoA synthase1 PublicationUniRule annotation
    Gene namesi
    Name:menBUniRule annotation
    Ordered Locus Names:b2262, JW2257
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11368. menB.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi89 – 891K → A: Strongly decreases affinity for substrate and DHNA-CoA synthase activity. 1 Publication
    Mutagenesisi91 – 911R → A: Loss of DHNA-CoA synthase activity. 1 Publication
    Mutagenesisi97 – 971Y → F: Loss of DHNA-CoA synthase activity. 1 Publication
    Mutagenesisi154 – 1541Q → A: Reduces the specific DHNA-CoA synthase activity by 15-fold, whereas its affinity for bicarbonate is reduced by 36-fold. 1 Publication
    Mutagenesisi156 – 1561G → D: Loss of DHNA-CoA synthase activity. 2 Publications
    Mutagenesisi184 – 1841W → F: Reduces the specific DHNA-CoA synthase activity by 530-fold, whereas its affinity for bicarbonate is reduced by 20-fold. 1 Publication
    Mutagenesisi267 – 2671R → A: Strongly decreases affinity for substrate and DHNA-CoA synthase activity. 1 Publication
    Mutagenesisi270 – 2701F → A: Strongly decreases affinity for substrate and DHNA-CoA synthase activity. 1 Publication
    Mutagenesisi273 – 2731K → A: Impairs protein folding. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2852851,4-dihydroxy-2-naphthoyl-CoA synthasePRO_0000109325Add
    BLAST

    Proteomic databases

    EPDiP0ABU0.
    PaxDbiP0ABU0.
    PRIDEiP0ABU0.

    Interactioni

    Subunit structurei

    Homohexamer. Dimer of a homotrimer.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    hldDP679102EBI-554195,EBI-543760

    Protein-protein interaction databases

    BioGridi4260504. 14 interactions.
    DIPiDIP-47854N.
    IntActiP0ABU0. 6 interactions.
    MINTiMINT-1227416.
    STRINGi511145.b2262.

    Structurei

    Secondary structure

    1
    285
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 94Combined sources
    Beta strandi15 – 173Combined sources
    Beta strandi23 – 308Combined sources
    Beta strandi33 – 397Combined sources
    Helixi42 – 443Combined sources
    Helixi50 – 6516Combined sources
    Beta strandi71 – 8313Combined sources
    Helixi88 – 903Combined sources
    Beta strandi93 – 986Combined sources
    Turni105 – 1073Combined sources
    Helixi108 – 11710Combined sources
    Beta strandi122 – 1265Combined sources
    Beta strandi128 – 1314Combined sources
    Helixi133 – 1408Combined sources
    Beta strandi141 – 1477Combined sources
    Beta strandi151 – 1533Combined sources
    Helixi156 – 1594Combined sources
    Turni166 – 1683Combined sources
    Helixi169 – 1757Combined sources
    Helixi177 – 18610Combined sources
    Helixi192 – 1976Combined sources
    Beta strandi200 – 2056Combined sources
    Helixi207 – 2093Combined sources
    Helixi210 – 22213Combined sources
    Helixi226 – 23813Combined sources
    Helixi242 – 25817Combined sources
    Helixi261 – 27111Combined sources
    Helixi278 – 2803Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3T88X-ray2.00A/B/C/D/E/F1-285[»]
    3T89X-ray1.95A/B/C/D/E/F1-285[»]
    4ELSX-ray2.30A/B/C/D/E/F1-285[»]
    4ELWX-ray2.55A/B/C/D/E/F1-285[»]
    4ELXX-ray2.19A/B/C/D/E/F1-285[»]
    4I42X-ray1.85A/B/C/D/E/F/G/H/I/J/K/L1-285[»]
    ProteinModelPortaliP0ABU0.
    SMRiP0ABU0. Positions 1-285.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni84 – 896Substrate binding2 Publications
    Regioni129 – 1335Substrate bindingUniRule annotation2 Publications
    Regioni154 – 1563Bicarbonate bindingUniRule annotation1 Publication

    Sequence similaritiesi

    Belongs to the enoyl-CoA hydratase/isomerase family. MenB subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4108IPT. Bacteria.
    COG0447. LUCA.
    HOGENOMiHOG000027942.
    InParanoidiP0ABU0.
    KOiK01661.
    OMAiKYAFCSG.
    PhylomeDBiP0ABU0.

    Family and domain databases

    Gene3Di1.10.12.10. 1 hit.
    3.90.226.10. 1 hit.
    HAMAPiMF_01934. MenB. 1 hit.
    InterProiIPR029045. ClpP/crotonase-like_dom.
    IPR014748. Crontonase_C.
    IPR001753. Crotonase_core_superfam.
    IPR010198. DHNA-CoA_synthase_MenB.
    IPR018376. Enoyl-CoA_hyd/isom_CS.
    [Graphical view]
    PfamiPF00378. ECH_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF52096. SSF52096. 1 hit.
    TIGRFAMsiTIGR01929. menB. 1 hit.
    PROSITEiPS00166. ENOYL_COA_HYDRATASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0ABU0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIYPDEAMLY APVEWHDCSE GFEDIRYEKS TDGIAKITIN RPQVRNAFRP
    60 70 80 90 100
    LTVKEMIQAL ADARYDDNIG VIILTGAGDK AFCSGGDQKV RGDYGGYKDD
    110 120 130 140 150
    SGVHHLNVLD FQRQIRTCPK PVVAMVAGYS IGGGHVLHMM CDLTIAADNA
    160 170 180 190 200
    IFGQTGPKVG SFDGGWGASY MARIVGQKKA REIWFLCRQY DAKQALDMGL
    210 220 230 240 250
    VNTVVPLADL EKETVRWCRE MLQNSPMALR CLKAALNADC DGQAGLQELA
    260 270 280
    GNATMLFYMT EEGQEGRNAF NQKRQPDFSK FKRNP
    Length:285
    Mass (Da):31,633
    Last modified:October 25, 2005 - v1
    Checksum:iC38E7206924408E6
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M93421 Genomic DNA. Translation: AAA23682.1.
    U00096 Genomic DNA. Translation: AAC75322.1.
    AP009048 Genomic DNA. Translation: BAA16086.1.
    L35030 Genomic DNA. Translation: AAA24152.1.
    PIRiA42714. D64997.
    RefSeqiNP_416765.1. NC_000913.3.
    WP_000639996.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75322; AAC75322; b2262.
    BAA16086; BAA16086; BAA16086.
    GeneIDi946747.
    KEGGiecj:JW2257.
    eco:b2262.
    PATRICi32119891. VBIEscCol129921_2355.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M93421 Genomic DNA. Translation: AAA23682.1.
    U00096 Genomic DNA. Translation: AAC75322.1.
    AP009048 Genomic DNA. Translation: BAA16086.1.
    L35030 Genomic DNA. Translation: AAA24152.1.
    PIRiA42714. D64997.
    RefSeqiNP_416765.1. NC_000913.3.
    WP_000639996.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3T88X-ray2.00A/B/C/D/E/F1-285[»]
    3T89X-ray1.95A/B/C/D/E/F1-285[»]
    4ELSX-ray2.30A/B/C/D/E/F1-285[»]
    4ELWX-ray2.55A/B/C/D/E/F1-285[»]
    4ELXX-ray2.19A/B/C/D/E/F1-285[»]
    4I42X-ray1.85A/B/C/D/E/F/G/H/I/J/K/L1-285[»]
    ProteinModelPortaliP0ABU0.
    SMRiP0ABU0. Positions 1-285.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260504. 14 interactions.
    DIPiDIP-47854N.
    IntActiP0ABU0. 6 interactions.
    MINTiMINT-1227416.
    STRINGi511145.b2262.

    Proteomic databases

    EPDiP0ABU0.
    PaxDbiP0ABU0.
    PRIDEiP0ABU0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75322; AAC75322; b2262.
    BAA16086; BAA16086; BAA16086.
    GeneIDi946747.
    KEGGiecj:JW2257.
    eco:b2262.
    PATRICi32119891. VBIEscCol129921_2355.

    Organism-specific databases

    EchoBASEiEB1342.
    EcoGeneiEG11368. menB.

    Phylogenomic databases

    eggNOGiENOG4108IPT. Bacteria.
    COG0447. LUCA.
    HOGENOMiHOG000027942.
    InParanoidiP0ABU0.
    KOiK01661.
    OMAiKYAFCSG.
    PhylomeDBiP0ABU0.

    Enzyme and pathway databases

    UniPathwayiUPA00079.
    UPA01057; UER00167.
    BioCyciEcoCyc:NAPHTHOATE-SYN-MONOMER.
    ECOL316407:JW2257-MONOMER.
    MetaCyc:NAPHTHOATE-SYN-MONOMER.

    Miscellaneous databases

    PROiP0ABU0.

    Family and domain databases

    Gene3Di1.10.12.10. 1 hit.
    3.90.226.10. 1 hit.
    HAMAPiMF_01934. MenB. 1 hit.
    InterProiIPR029045. ClpP/crotonase-like_dom.
    IPR014748. Crontonase_C.
    IPR001753. Crotonase_core_superfam.
    IPR010198. DHNA-CoA_synthase_MenB.
    IPR018376. Enoyl-CoA_hyd/isom_CS.
    [Graphical view]
    PfamiPF00378. ECH_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF52096. SSF52096. 1 hit.
    TIGRFAMsiTIGR01929. menB. 1 hit.
    PROSITEiPS00166. ENOYL_COA_HYDRATASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiMENB_ECOLI
    AccessioniPrimary (citable) accession number: P0ABU0
    Secondary accession number(s): P27290
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 25, 2005
    Last sequence update: October 25, 2005
    Last modified: September 7, 2016
    This is version 92 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.