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Q55012

- PENA_STREX

UniProt

Q55012 - PENA_STREX

Protein

Pentalenene synthase

Gene

penA

Organism
Streptomyces exfoliatus (Streptomyces hydrogenans)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 80 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalyzes the cyclization of farnesyl diphosphate (FPP) to the tricyclic sesquiterpene pentalenene, which is the hydrocarbon precursor of the pentalenolactone family of antibiotics produced by a variety of Streptomyces species.1 Publication

    Catalytic activityi

    (2E,6E)-farnesyl diphosphate = pentalenene + diphosphate.1 Publication

    Cofactori

    Binds 3 magnesium ions per subunit.By similarity

    Kineticsi

    1. KM=310 nM for FPP1 Publication

    pH dependencei

    Optimum pH is 8.2-8.4.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi80 – 801Magnesium 1
    Metal bindingi80 – 801Magnesium 2
    Metal bindingi84 – 841Magnesium 1
    Metal bindingi84 – 841Magnesium 2
    Metal bindingi219 – 2191Magnesium 3
    Metal bindingi223 – 2231Magnesium 3By similarity
    Metal bindingi227 – 2271Magnesium 3By similarity

    GO - Molecular functioni

    1. magnesium ion binding Source: InterPro
    2. pentalenene synthase activity Source: UniProtKB-EC

    GO - Biological processi

    1. antibiotic biosynthetic process Source: UniProtKB-KW

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16834.
    BRENDAi4.2.3.7. 6094.
    UniPathwayiUPA00171; UER00581.
    UPA00974.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pentalenene synthase (EC:4.2.3.7)
    Short name:
    PS
    Alternative name(s):
    Pentalenolactone biosynthesis protein A
    Sesquiterpene cyclase
    Sesquiterpene synthase
    Gene namesi
    Name:penA
    OrganismiStreptomyces exfoliatus (Streptomyces hydrogenans)
    Taxonomic identifieri1905 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesStreptomycineaeStreptomycetaceaeStreptomyces

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi76 – 761F → A: Loss of activity. 1 Publication
    Mutagenesisi77 – 771F → A: Loss of activity. 1 Publication
    Mutagenesisi77 – 771F → Y: 20-fold decrease in activity and catalytic efficiency. 1 Publication
    Mutagenesisi80 – 801D → E: 150-fold decrease in activity. 20-fold increase in Km for FPP. 1 Publication
    Mutagenesisi81 – 811D → E: 50-fold decrease in activity. 9-fold increase in Km for FPP. 1 Publication
    Mutagenesisi84 – 841D → E: 2.5-fold increase in activity. 7-fold increase in Km for FPP. 1 Publication
    Mutagenesisi219 – 2191N → A: Loss of activity. 1 Publication
    Mutagenesisi219 – 2191N → D: 60-fold decrease in activity. 55-fold increase in Km for FPP. 1 Publication
    Mutagenesisi219 – 2191N → L: Loss of activity. 1 Publication
    Mutagenesisi308 – 3092WH → FF: 12-fold decrease in activity. 25-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi308 – 3081W → F: 4-fold decrease in activity. 2-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi309 – 3091H → A: 3-fold decrease in activity. 2 Publications
    Mutagenesisi309 – 3091H → C: 4-fold decrease in activity. 2 Publications
    Mutagenesisi309 – 3091H → F: 17-fold decrease in activity. 5-fold increase in Km for FPP. 2 Publications
    Mutagenesisi309 – 3091H → S: 3-fold decrease in activity. 2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 337336Pentalenene synthasePRO_0000097092Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi128 ↔ 136

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Structurei

    Secondary structure

    1
    337
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi19 – 246
    Helixi28 – 325
    Helixi39 – 468
    Helixi50 – 578
    Helixi64 – 8118
    Helixi86 – 894
    Helixi91 – 10212
    Helixi103 – 1053
    Helixi115 – 12814
    Helixi133 – 15422
    Helixi166 – 17611
    Helixi179 – 19012
    Helixi196 – 1994
    Helixi202 – 22221
    Helixi224 – 2296
    Helixi236 – 2449
    Helixi248 – 27932
    Helixi284 – 29613
    Helixi298 – 30811
    Turni309 – 3113

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1HM4X-ray3.47A/B2-337[»]
    1HM7X-ray2.90A/B2-337[»]
    1PS1X-ray2.60A/B1-337[»]
    ProteinModelPortaliQ55012.
    SMRiQ55012. Positions 7-311.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ55012.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi80 – 845DDXXD motif

    Domaini

    The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg2+.

    Sequence similaritiesi

    Belongs to the terpene synthase family.Curated

    Family and domain databases

    Gene3Di1.10.600.10. 1 hit.
    InterProiIPR005630. Terpene_synthase_metal-bd.
    IPR008949. Terpenoid_synth.
    [Graphical view]
    PfamiPF03936. Terpene_synth_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF48576. SSF48576. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q55012-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPQDVDFHIP LPGRQSPDHA RAEAEQLAWP RSLGLIRSDA AAERHLRGGY    50
    ADLASRFYPH ATGADLDLGV DLMSWFFLFD DLFDGPRGEN PEDTKQLTDQ 100
    VAAALDGPLP DTAPPIAHGF ADIWRRTCEG MTPAWCARSA RHWRNYFDGY 150
    VDEAESRFWN APCDSAAQYL AMRRHTIGVQ PTVDLAERAG RFEVPHRVFD 200
    SAVMSAMLQI AVDVNLLLND IASLEKEEAR GEQNNMVMIL RREHGWSKSR 250
    SVSHMQNEVR ARLEQYLLLE SCLPKVGEIY QLDTAEREAL ERYRTDAVRT 300
    VIRGSYDWHR SSGRYDAEFA LAAGAQGYLE ELGSSAH 337
    Length:337
    Mass (Da):38,002
    Last modified:January 23, 2007 - v4
    Checksum:i417FCE6D8C4BB18C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti118 – 1181H → W AA sequence (PubMed:8180213)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U05213 Unassigned DNA. Translation: AAA19131.1.
    HQ292066 Genomic DNA. Translation: ADO85594.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U05213 Unassigned DNA. Translation: AAA19131.1 .
    HQ292066 Genomic DNA. Translation: ADO85594.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1HM4 X-ray 3.47 A/B 2-337 [» ]
    1HM7 X-ray 2.90 A/B 2-337 [» ]
    1PS1 X-ray 2.60 A/B 1-337 [» ]
    ProteinModelPortali Q55012.
    SMRi Q55012. Positions 7-311.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00171 ; UER00581 .
    UPA00974 .
    BioCyci MetaCyc:MONOMER-16834.
    BRENDAi 4.2.3.7. 6094.

    Miscellaneous databases

    EvolutionaryTracei Q55012.

    Family and domain databases

    Gene3Di 1.10.600.10. 1 hit.
    InterProi IPR005630. Terpene_synthase_metal-bd.
    IPR008949. Terpenoid_synth.
    [Graphical view ]
    Pfami PF03936. Terpene_synth_C. 1 hit.
    [Graphical view ]
    SUPFAMi SSF48576. SSF48576. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Pentalenene synthase. Purification, molecular cloning, sequencing, and high-level expression in Escherichia coli of a terpenoid cyclase from Streptomyces UC5319."
      Cane D.E., Sohng J.-K., Lamberson C.R., Rudnicki S.M., Wu Z., Lloyd M.D., Oliver J.S., Hubbard B.R.
      Biochemistry 33:5846-5857(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-28; 57-73; 96-120 AND 145-157, FUNCTION, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: UC5319.
    2. "Genome mining in streptomyces. Discovery of an unprecedented P450-catalyzed oxidative rearrangement that is the final step in the biosynthesis of pentalenolactone."
      Zhu D., Seo M.J., Ikeda H., Cane D.E.
      J. Am. Chem. Soc. 133:2128-2131(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: UC5319.
    3. "Pentalenene synthase. Histidine-309 is not required for catalytic activity."
      Seemann M., Zhai G., Umezawa K., Cane D.E.
      J. Am. Chem. Soc. 121:591-592(1999)
      Cited for: MUTAGENESIS OF HIS-309.
    4. "Crystal structure of pentalenene synthase: mechanistic insights on terpenoid cyclization reactions in biology."
      Lesburg C.A., Zhai G., Cane D.E., Christianson D.W.
      Science 277:1820-1824(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
    5. "Pentalenene synthase. Analysis of active site residues by site-directed mutagenesis."
      Seemann M., Zhai G., de Kraker J.-W., Paschall C.M., Christianson D.W., Cane D.E.
      J. Am. Chem. Soc. 124:7681-7689(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF MUTANT LEU-219, CATALYTIC ACTIVITY, MUTAGENESIS OF PHE-76; PHE-77; ASP-80; ASP-81; ASP-84; ASN-219; 308-TRP-HIS-309; TRP-308 AND HIS-309.

    Entry informationi

    Entry nameiPENA_STREX
    AccessioniPrimary (citable) accession number: Q55012
    Secondary accession number(s): E3VWK6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 80 of the entry and version 4 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    All the mutants (PubMed:9295272 and PubMed:12083921) retained substantial pentalenene synthase activity accompanied by production of varying proportions of abortive cyclization products such as germacrene A, protoilludene and beta-caryophyllene. This is a true derailment or diversion of the normal cyclization reaction, and not simply the consequence of trapping of a normally cryptic, cationic intermediate.

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3