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Protein

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

Gene

menB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

hydrogencarbonateUniRule annotation1 Publication1 PublicationNote: The hydrogencarbonate 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

Activity 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)DescriptionActionsGraphical viewLength
    Binding sitei45SubstrateUniRule annotation2 Publications1
    Binding sitei97SubstrateUniRule annotation1 Publication1
    Sitei97Important for catalysisUniRule annotation1 Publication1
    Binding sitei155SubstrateUniRule annotation2 Publications1
    Binding sitei161SubstrateUniRule annotation1 Publication1
    Binding sitei258Substrate; shared with neighboring subunitUniRule annotation1 Publication1
    Sitei258Important for catalysisUniRule annotation1 Publication1
    Binding sitei273Substrate; shared with neighboring subunitUniRule annotation2 Publications1

    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

    Keywordsi

    Molecular functionLyase
    Biological processMenaquinone biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:NAPHTHOATE-SYN-MONOMER
    MetaCyc:NAPHTHOATE-SYN-MONOMER
    UniPathwayi
    UPA00079

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11368 menB

    Subcellular locationi

    GO - Cellular componenti

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi89K → A: Strongly decreases affinity for substrate and DHNA-CoA synthase activity. 1 Publication1
    Mutagenesisi91R → A: Loss of DHNA-CoA synthase activity. 1 Publication1
    Mutagenesisi97Y → F: Loss of DHNA-CoA synthase activity. 1 Publication1
    Mutagenesisi154Q → A: Reduces the specific DHNA-CoA synthase activity by 15-fold, whereas its affinity for hydrogencarbonate is reduced by 36-fold. 1 Publication1
    Mutagenesisi156G → D: Loss of DHNA-CoA synthase activity. 2 Publications1
    Mutagenesisi184W → F: Reduces the specific DHNA-CoA synthase activity by 530-fold, whereas its affinity for hydrogencarbonate is reduced by 20-fold. 1 Publication1
    Mutagenesisi267R → A: Strongly decreases affinity for substrate and DHNA-CoA synthase activity. 1 Publication1
    Mutagenesisi270F → A: Strongly decreases affinity for substrate and DHNA-CoA synthase activity. 1 Publication1
    Mutagenesisi273K → A: Impairs protein folding. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001093251 – 2851,4-dihydroxy-2-naphthoyl-CoA synthaseAdd BLAST285

    Proteomic databases

    EPDiP0ABU0
    PaxDbiP0ABU0
    PRIDEiP0ABU0

    Interactioni

    Subunit structurei

    Homohexamer. Dimer of a homotrimer.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    hldDP679103EBI-554195,EBI-543760

    Protein-protein interaction databases

    BioGridi4260504, 18 interactors
    DIPiDIP-47854N
    IntActiP0ABU0, 6 interactors
    STRINGi316385.ECDH10B_2423

    Structurei

    Secondary structure

    1285
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP0ABU0
    SMRiP0ABU0
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni84 – 89Substrate binding2 Publications6
    Regioni129 – 133Substrate bindingUniRule annotation2 Publications5
    Regioni154 – 156Hydrogencarbonate bindingUniRule annotation1 Publication3

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4108IPT Bacteria
    COG0447 LUCA
    HOGENOMiHOG000027942
    InParanoidiP0ABU0
    KOiK01661
    OMAiIFKQTDA
    PhylomeDBiP0ABU0

    Family and domain databases

    Gene3Di1.10.12.10, 1 hit
    HAMAPiMF_01934 MenB, 1 hit
    InterProiView protein in InterPro
    IPR029045 ClpP/crotonase-like_dom_sf
    IPR010198 DHNA-CoA_synthase_MenB
    IPR018376 Enoyl-CoA_hyd/isom_CS
    IPR001753 Enoyl-CoA_hydra/iso
    IPR014748 Enoyl-CoA_hydra_C
    PANTHERiPTHR43113 PTHR43113, 1 hit
    PfamiView protein in Pfam
    PF00378 ECH_1, 1 hit
    SUPFAMiSSF52096 SSF52096, 1 hit
    TIGRFAMsiTIGR01929 menB, 1 hit
    PROSITEiView protein in PROSITE
    PS00166 ENOYL_COA_HYDRATASE, 1 hit

    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
    PATRICifig|511145.12.peg.2355

    Similar proteinsi

    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
    PDB 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
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260504, 18 interactors
    DIPiDIP-47854N
    IntActiP0ABU0, 6 interactors
    STRINGi316385.ECDH10B_2423

    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
    PATRICifig|511145.12.peg.2355

    Organism-specific databases

    EchoBASEiEB1342
    EcoGeneiEG11368 menB

    Phylogenomic databases

    eggNOGiENOG4108IPT Bacteria
    COG0447 LUCA
    HOGENOMiHOG000027942
    InParanoidiP0ABU0
    KOiK01661
    OMAiIFKQTDA
    PhylomeDBiP0ABU0

    Enzyme and pathway databases

    UniPathwayi
    UPA00079

    UPA01057;UER00167

    BioCyciEcoCyc:NAPHTHOATE-SYN-MONOMER
    MetaCyc:NAPHTHOATE-SYN-MONOMER

    Miscellaneous databases

    PROiPR:P0ABU0

    Family and domain databases

    Gene3Di1.10.12.10, 1 hit
    HAMAPiMF_01934 MenB, 1 hit
    InterProiView protein in InterPro
    IPR029045 ClpP/crotonase-like_dom_sf
    IPR010198 DHNA-CoA_synthase_MenB
    IPR018376 Enoyl-CoA_hyd/isom_CS
    IPR001753 Enoyl-CoA_hydra/iso
    IPR014748 Enoyl-CoA_hydra_C
    PANTHERiPTHR43113 PTHR43113, 1 hit
    PfamiView protein in Pfam
    PF00378 ECH_1, 1 hit
    SUPFAMiSSF52096 SSF52096, 1 hit
    TIGRFAMsiTIGR01929 menB, 1 hit
    PROSITEiView protein in PROSITE
    PS00166 ENOYL_COA_HYDRATASE, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiMENB_ECOLI
    AccessioniPrimary (citable) accession number: P0ABU0
    Secondary accession number(s): P27290
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 25, 2005
    Last sequence update: October 25, 2005
    Last modified: September 12, 2018
    This is version 108 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
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