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Protein

Pimeloyl-[acyl-carrier protein] methyl ester esterase

Gene

bioH

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

Functioni

The physiological role of BioH is to remove the methyl group introduced by BioC when the pimeloyl moiety is complete. It allows to synthesize pimeloyl-ACP via the fatty acid synthetic pathway through the hydrolysis of the ester bonds of pimeloyl-ACP esters. E.coli employs a methylation and demethylation strategy to allow elongation of a temporarily disguised malonate moiety to a pimelate moiety by the fatty acid synthetic enzymes. BioH shows a preference for short chain fatty acid esters (acyl chain length of up to 6 carbons) and short chain p-nitrophenyl esters. Also displays a weak thioesterase activity. Can form a complex with CoA, and may be involved in the condensation of CoA and pimelic acid into pimeloyl-CoA, a precursor in biotin biosynthesis.
Catalyzes the hydrolysis of the methyl ester bond of dimethylbutyryl-S-methyl mercaptopropionate (DMB-S-MMP) to yield dimethylbutyryl mercaptopropionic acid (DMBS-MPA) during the biocatalytic conversion of simvastin acid from monacolin J acid. Can also use acyl carriers such as dimethylbutyryl-S-ethyl mercaptopropionate (DMB-S-EMP) and dimethylbutyryl-S-methyl thioglycolate (DMB-S-MTG) as the thioester substrates.

Catalytic activityi

Pimeloyl-[acyl-carrier protein] methyl ester + H2O = pimeloyl-[acyl-carrier protein] + methanol.1 Publication

Enzyme regulationi

Strongly inhibited by phenylmethylsulfonyl fluoride (PMSF).

Kineticsi

The highest catalytic efficiency was observed with pNP-acetate, then with pNP-propionate, pNP-butyrate and pNP-caproate.

  1. KM=229 µM for DMB-S-MMP (at Ph 7.9 and at room temperature)3 Publications
  2. KM=0.29 mM for pNP-acetate3 Publications
  3. KM=0.35 mM for pNP-propionate3 Publications
  4. KM=0.33 mM for pNP-butyrate3 Publications
  5. KM=0.25 mM for pNP-caproate3 Publications
  6. KM=0.60 mM for pNP-laurate3 Publications

    pH dependencei

    Optimum pH is 8.0-8.5. The activity is more than 90% in the pH range from 7 to 9.3 Publications

    Temperature dependencei

    Optimum temperature is between 20 and 30 degrees Celsius.3 Publications

    Pathwayi: biotin biosynthesis

    This protein is involved in the pathway biotin biosynthesis, which is part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the pathway biotin biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei22Substrate; via amide nitrogen and carbonyl oxygen1
    Active sitei82Nucleophile1
    Active sitei207By similarity1
    Active sitei2351
    Binding sitei235Substrate1

    GO - Molecular functioni

    • carboxylic ester hydrolase activity Source: UniProtKB
    • pimelyl-[acyl-carrier protein] methyl ester esterase activity Source: EcoCyc

    GO - Biological processi

    • biotin biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Serine esterase

    Keywords - Biological processi

    Biotin biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10122-MONOMER.
    ECOL316407:JW3375-MONOMER.
    MetaCyc:EG10122-MONOMER.
    BRENDAi3.1.1.1. 2026.
    3.1.1.85. 2026.
    SABIO-RKP13001.
    UniPathwayiUPA00078.

    Protein family/group databases

    ESTHERiecoli-bioh. BioH.
    MEROPSiS33.994.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pimeloyl-[acyl-carrier protein] methyl ester esterase (EC:3.1.1.85)
    Alternative name(s):
    Biotin synthesis protein BioH
    Carboxylesterase BioH
    Gene namesi
    Name:bioH
    Synonyms:bioB
    Ordered Locus Names:b3412, JW3375
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10122. bioH.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Cells display no detectable hydrolysis of the thioester and no trace of DMB-S-MPA.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi82S → A: No effect on CoA-binding. Loss of Carboxylesterase activity. 2 Publications1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002044731 – 256Pimeloyl-[acyl-carrier protein] methyl ester esteraseAdd BLAST256

    Proteomic databases

    PaxDbiP13001.
    PRIDEiP13001.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    BioGridi4263494. 14 interactors.
    DIPiDIP-9223N.
    IntActiP13001. 4 interactors.
    MINTiMINT-1253056.
    STRINGi511145.b3412.

    Structurei

    Secondary structure

    1256
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi6 – 9Combined sources4
    Beta strandi13 – 19Combined sources7
    Helixi26 – 31Combined sources6
    Helixi33 – 37Combined sources5
    Beta strandi40 – 45Combined sources6
    Helixi61 – 69Combined sources9
    Beta strandi74 – 81Combined sources8
    Helixi83 – 94Combined sources12
    Helixi96 – 98Combined sources3
    Beta strandi99 – 106Combined sources8
    Helixi122 – 145Combined sources24
    Helixi154 – 166Combined sources13
    Helixi173 – 185Combined sources13
    Helixi191 – 194Combined sources4
    Beta strandi199 – 204Combined sources6
    Beta strandi208 – 210Combined sources3
    Helixi214 – 221Combined sources8
    Beta strandi226 – 230Combined sources5
    Helixi237 – 240Combined sources4
    Helixi242 – 253Combined sources12

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1M33X-ray1.70A1-256[»]
    ProteinModelPortaliP13001.
    SMRiP13001.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13001.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini15 – 242AB hydrolase-1Sequence analysisAdd BLAST228

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni82 – 83Substrate binding2
    Regioni143 – 147Substrate binding5

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105D3C. Bacteria.
    COG0596. LUCA.
    HOGENOMiHOG000028062.
    InParanoidiP13001.
    KOiK02170.
    OMAiLICELIS.
    PhylomeDBiP13001.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01260. Carboxylester. 1 hit.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    IPR010076. BioH.
    [Graphical view]
    PfamiPF00561. Abhydrolase_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53474. SSF53474. 1 hit.
    TIGRFAMsiTIGR01738. bioH. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P13001-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNNIWWQTKG QGNVHLVLLH GWGLNAEVWR CIDEELSSHF TLHLVDLPGF
    60 70 80 90 100
    GRSRGFGALS LADMAEAVLQ QAPDKAIWLG WSLGGLVASQ IALTHPERVQ
    110 120 130 140 150
    ALVTVASSPC FSARDEWPGI KPDVLAGFQQ QLSDDFQRTV ERFLALQTMG
    160 170 180 190 200
    TETARQDARA LKKTVLALPM PEVDVLNGGL EILKTVDLRQ PLQNVSMPFL
    210 220 230 240 250
    RLYGYLDGLV PRKVVPMLDK LWPHSESYIF AKAAHAPFIS HPAEFCHLLV

    ALKQRV
    Length:256
    Mass (Da):28,505
    Last modified:January 1, 1990 - v1
    Checksum:i931226F241BBCBF3
    GO

    Mass spectrometryi

    Molecular mass is 28502.0±5.5 Da from positions 1 - 256. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X15587 Genomic DNA. Translation: CAA33612.1.
    U18997 Genomic DNA. Translation: AAA58210.1.
    U00096 Genomic DNA. Translation: AAC76437.1.
    AP009048 Genomic DNA. Translation: BAE77879.1.
    PIRiJQ0081. BVECBH.
    RefSeqiNP_417871.1. NC_000913.3.
    WP_001060070.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76437; AAC76437; b3412.
    BAE77879; BAE77879; BAE77879.
    GeneIDi947916.
    KEGGiecj:JW3375.
    eco:b3412.
    PATRICi32122260. VBIEscCol129921_3507.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X15587 Genomic DNA. Translation: CAA33612.1.
    U18997 Genomic DNA. Translation: AAA58210.1.
    U00096 Genomic DNA. Translation: AAC76437.1.
    AP009048 Genomic DNA. Translation: BAE77879.1.
    PIRiJQ0081. BVECBH.
    RefSeqiNP_417871.1. NC_000913.3.
    WP_001060070.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1M33X-ray1.70A1-256[»]
    ProteinModelPortaliP13001.
    SMRiP13001.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4263494. 14 interactors.
    DIPiDIP-9223N.
    IntActiP13001. 4 interactors.
    MINTiMINT-1253056.
    STRINGi511145.b3412.

    Protein family/group databases

    ESTHERiecoli-bioh. BioH.
    MEROPSiS33.994.

    Proteomic databases

    PaxDbiP13001.
    PRIDEiP13001.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76437; AAC76437; b3412.
    BAE77879; BAE77879; BAE77879.
    GeneIDi947916.
    KEGGiecj:JW3375.
    eco:b3412.
    PATRICi32122260. VBIEscCol129921_3507.

    Organism-specific databases

    EchoBASEiEB0120.
    EcoGeneiEG10122. bioH.

    Phylogenomic databases

    eggNOGiENOG4105D3C. Bacteria.
    COG0596. LUCA.
    HOGENOMiHOG000028062.
    InParanoidiP13001.
    KOiK02170.
    OMAiLICELIS.
    PhylomeDBiP13001.

    Enzyme and pathway databases

    UniPathwayiUPA00078.
    BioCyciEcoCyc:EG10122-MONOMER.
    ECOL316407:JW3375-MONOMER.
    MetaCyc:EG10122-MONOMER.
    BRENDAi3.1.1.1. 2026.
    3.1.1.85. 2026.
    SABIO-RKP13001.

    Miscellaneous databases

    EvolutionaryTraceiP13001.
    PROiP13001.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01260. Carboxylester. 1 hit.
    InterProiIPR029058. AB_hydrolase.
    IPR000073. AB_hydrolase_1.
    IPR010076. BioH.
    [Graphical view]
    PfamiPF00561. Abhydrolase_1. 1 hit.
    [Graphical view]
    SUPFAMiSSF53474. SSF53474. 1 hit.
    TIGRFAMsiTIGR01738. bioH. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiBIOH_ECOLI
    AccessioniPrimary (citable) accession number: P13001
    Secondary accession number(s): Q2M777
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 1, 1990
    Last sequence update: January 1, 1990
    Last modified: November 2, 2016
    This is version 142 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.