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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei22 – 221Substrate; via amide nitrogen and carbonyl oxygen
    Active sitei82 – 821Nucleophile
    Active sitei207 – 2071By similarity
    Active sitei235 – 2351
    Binding sitei235 – 2351Substrate

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi82 – 821S → A: No effect on CoA-binding. Loss of Carboxylesterase activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 256256Pimeloyl-[acyl-carrier protein] methyl ester esterasePRO_0000204473Add
    BLAST

    Proteomic databases

    PaxDbiP13001.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1
    256
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 94Combined sources
    Beta strandi13 – 197Combined sources
    Helixi26 – 316Combined sources
    Helixi33 – 375Combined sources
    Beta strandi40 – 456Combined sources
    Helixi61 – 699Combined sources
    Beta strandi74 – 818Combined sources
    Helixi83 – 9412Combined sources
    Helixi96 – 983Combined sources
    Beta strandi99 – 1068Combined sources
    Helixi122 – 14524Combined sources
    Helixi154 – 16613Combined sources
    Helixi173 – 18513Combined sources
    Helixi191 – 1944Combined sources
    Beta strandi199 – 2046Combined sources
    Beta strandi208 – 2103Combined sources
    Helixi214 – 2218Combined sources
    Beta strandi226 – 2305Combined sources
    Helixi237 – 2404Combined sources
    Helixi242 – 25312Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1M33X-ray1.70A1-256[»]
    ProteinModelPortaliP13001.
    SMRiP13001. Positions 3-256.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP13001.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni82 – 832Substrate binding
    Regioni143 – 1475Substrate binding

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105D3C. Bacteria.
    COG0596. LUCA.
    HOGENOMiHOG000028062.
    InParanoidiP13001.
    KOiK02170.
    OMAiLICELIS.
    OrthoDBiEOG6FJNH9.
    PhylomeDBiP13001.

    Family and domain databases

    Gene3Di3.40.50.1820. 1 hit.
    HAMAPiMF_01260. Carboxylester.
    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1M33X-ray1.70A1-256[»]
    ProteinModelPortaliP13001.
    SMRiP13001. Positions 3-256.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Protein family/group databases

    ESTHERiecoli-bioh. BioH.
    MEROPSiS33.994.

    Proteomic databases

    PaxDbiP13001.

    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.
    OrthoDBiEOG6FJNH9.
    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.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    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. "Purification and characterisation of the BIOH protein from the biotin biosynthetic pathway."
      Tomczyk N.H., Nettleship J.E., Baxter R.L., Crichton H.J., Webster S.P., Campopiano D.J.
      FEBS Lett. 513:299-304(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN THE BIOTIN BIOSYNTHESIS, CATALYTIC ACTIVITY, BINDING TO COA, SUBUNIT, MASS SPECTROMETRY, MUTAGENESIS OF SER-82.
      Strain: K12 / JM101 / ATCC 33876 / DSM 3948 / NCIMB 11926.
    5. "Improving simvastatin bioconversion in Escherichia coli by deletion of bioH."
      Xie X., Wong W.W., Tang Y.
      Metab. Eng. 9:379-386(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A CARBOXYLESTERASE AND IN THE SIMVASTATIN BIOCONVERSION, DISRUPTION PHENOTYPE, BIOPHYSICOCHEMICAL PROPERTIES.
    6. "Gene cloning, expression, and characterization of a new carboxylesterase from Serratia sp. SES-01: comparison with Escherichia coli BioHe enzyme."
      Kwon M.A., Kim H.S., Oh J.Y., Song B.K., Song J.K.
      J. Microbiol. Biotechnol. 19:147-154(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
    7. "Biotin synthesis begins by hijacking the fatty acid synthetic pathway."
      Lin S., Hanson R.E., Cronan J.E.
      Nat. Chem. Biol. 6:682-688(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A CARBOXYLESTERASE, MUTAGENESIS OF SER-82, SUBSTRATE SPECIFICITY.
    8. "Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli."
      Sanishvili R., Yakunin A.F., Laskowski R.A., Skarina T., Evdokimova E., Doherty-Kirby A., Lajoie G.A., Thornton J.M., Arrowsmith C.H., Savchenko A., Joachimiak A., Edwards A.M.
      J. Biol. Chem. 278:26039-26045(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS), FUNCTION AS A CARBOXYLESTERASE, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: K12 / DH5-alpha.

    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: January 20, 2016
    This is version 139 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.