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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

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

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

Manual assertion based on experiment ini

  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
    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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)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
    hldDP679102EBI-554195,EBI-543760

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1285
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 9Combined sources4
    Beta strandi15 – 17Combined sources3
    Beta strandi23 – 30Combined sources8
    Beta strandi33 – 39Combined sources7
    Helixi42 – 44Combined sources3
    Helixi50 – 65Combined sources16
    Beta strandi71 – 83Combined sources13
    Helixi88 – 90Combined sources3
    Beta strandi93 – 98Combined sources6
    Turni105 – 107Combined sources3
    Helixi108 – 117Combined sources10
    Beta strandi122 – 126Combined sources5
    Beta strandi128 – 131Combined sources4
    Helixi133 – 140Combined sources8
    Beta strandi141 – 147Combined sources7
    Beta strandi151 – 153Combined sources3
    Helixi156 – 159Combined sources4
    Turni166 – 168Combined sources3
    Helixi169 – 175Combined sources7
    Helixi177 – 186Combined sources10
    Helixi192 – 197Combined sources6
    Beta strandi200 – 205Combined sources6
    Helixi207 – 209Combined sources3
    Helixi210 – 222Combined sources13
    Helixi226 – 238Combined sources13
    Helixi242 – 258Combined sources17
    Helixi261 – 271Combined sources11
    Helixi278 – 280Combined sources3

    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...

    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.
    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
    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. 14 interactors.
    DIPiDIP-47854N.
    IntActiP0ABU0. 6 interactors.
    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: November 30, 2016
    This is version 95 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.