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Protein

Pentalenene synthase

Gene

penA

Organism
Streptomyces exfoliatus (Streptomyces hydrogenans)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Mg2+By similarityNote: Binds 3 Mg2+ 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: pentalenene biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes pentalenene from farnesyl diphosphate.
    Proteins known to be involved in this subpathway in this organism are:
    1. Pentalenene synthase (penA)
    This subpathway is part of the pathway pentalenene biosynthesis, which is itself part of Sesquiterpene biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes pentalenene from farnesyl diphosphate, the pathway pentalenene biosynthesis and in Sesquiterpene biosynthesis.

    Pathwayi: pentalenolactone biosynthesis

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

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi80Magnesium 11
    Metal bindingi80Magnesium 21
    Metal bindingi84Magnesium 11
    Metal bindingi84Magnesium 21
    Metal bindingi219Magnesium 31
    Metal bindingi223Magnesium 3By similarity1
    Metal bindingi227Magnesium 3By similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    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. 22521.
    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 lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi76F → A: Loss of activity. 1 Publication1
    Mutagenesisi77F → A: Loss of activity. 1 Publication1
    Mutagenesisi77F → Y: 20-fold decrease in activity and catalytic efficiency. 1 Publication1
    Mutagenesisi80D → E: 150-fold decrease in activity. 20-fold increase in Km for FPP. 1 Publication1
    Mutagenesisi81D → E: 50-fold decrease in activity. 9-fold increase in Km for FPP. 1 Publication1
    Mutagenesisi84D → E: 2.5-fold increase in activity. 7-fold increase in Km for FPP. 1 Publication1
    Mutagenesisi219N → A: Loss of activity. 1 Publication1
    Mutagenesisi219N → D: 60-fold decrease in activity. 55-fold increase in Km for FPP. 1 Publication1
    Mutagenesisi219N → L: Loss of activity. 1 Publication1
    Mutagenesisi308 – 309WH → FF: 12-fold decrease in activity. 25-fold decrease in catalytic efficiency. 1 Publication2
    Mutagenesisi308W → F: 4-fold decrease in activity. 2-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi309H → A: 3-fold decrease in activity. 2 Publications1
    Mutagenesisi309H → C: 4-fold decrease in activity. 2 Publications1
    Mutagenesisi309H → F: 17-fold decrease in activity. 5-fold increase in Km for FPP. 2 Publications1
    Mutagenesisi309H → S: 3-fold decrease in activity. 2 Publications1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00000970922 – 337Pentalenene synthaseAdd BLAST336

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Disulfide bondi128 ↔ 136

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Structurei

    Secondary structure

    1337
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi19 – 24Combined sources6
    Helixi28 – 32Combined sources5
    Helixi39 – 46Combined sources8
    Helixi50 – 57Combined sources8
    Helixi64 – 81Combined sources18
    Helixi86 – 89Combined sources4
    Helixi91 – 102Combined sources12
    Helixi103 – 105Combined sources3
    Helixi115 – 128Combined sources14
    Helixi133 – 154Combined sources22
    Helixi166 – 176Combined sources11
    Helixi179 – 190Combined sources12
    Helixi196 – 199Combined sources4
    Helixi202 – 222Combined sources21
    Helixi224 – 229Combined sources6
    Helixi236 – 244Combined sources9
    Helixi248 – 279Combined sources32
    Helixi284 – 296Combined sources13
    Helixi298 – 308Combined sources11
    Turni309 – 311Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1HM4X-ray3.47A/B2-337[»]
    1HM7X-ray2.90A/B2-337[»]
    1PS1X-ray2.60A/B1-337[»]
    ProteinModelPortaliQ55012.
    SMRiQ55012.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ55012.

    Family & Domainsi

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi80 – 84DDXXD motif5

    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.
    InterProiIPR008949. Isoprenoid_synthase_dom.
    [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

            10         20         30         40         50
    MPQDVDFHIP LPGRQSPDHA RAEAEQLAWP RSLGLIRSDA AAERHLRGGY
    60 70 80 90 100
    ADLASRFYPH ATGADLDLGV DLMSWFFLFD DLFDGPRGEN PEDTKQLTDQ
    110 120 130 140 150
    VAAALDGPLP DTAPPIAHGF ADIWRRTCEG MTPAWCARSA RHWRNYFDGY
    160 170 180 190 200
    VDEAESRFWN APCDSAAQYL AMRRHTIGVQ PTVDLAERAG RFEVPHRVFD
    210 220 230 240 250
    SAVMSAMLQI AVDVNLLLND IASLEKEEAR GEQNNMVMIL RREHGWSKSR
    260 270 280 290 300
    SVSHMQNEVR ARLEQYLLLE SCLPKVGEIY QLDTAEREAL ERYRTDAVRT
    310 320 330
    VIRGSYDWHR SSGRYDAEFA LAAGAQGYLE ELGSSAH
    Length:337
    Mass (Da):38,002
    Last modified:January 23, 2007 - v4
    Checksum:i417FCE6D8C4BB18C
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti118H → W AA sequence (PubMed:8180213).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U05213 Unassigned DNA. Translation: AAA19131.1.
    HQ292066 Genomic DNA. Translation: ADO85594.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U05213 Unassigned DNA. Translation: AAA19131.1.
    HQ292066 Genomic DNA. Translation: ADO85594.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1HM4X-ray3.47A/B2-337[»]
    1HM7X-ray2.90A/B2-337[»]
    1PS1X-ray2.60A/B1-337[»]
    ProteinModelPortaliQ55012.
    SMRiQ55012.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Enzyme and pathway databases

    UniPathwayiUPA00171; UER00581.
    UPA00974.
    BioCyciMetaCyc:MONOMER-16834.
    BRENDAi4.2.3.7. 22521.

    Miscellaneous databases

    EvolutionaryTraceiQ55012.

    Family and domain databases

    Gene3Di1.10.600.10. 1 hit.
    InterProiIPR008949. Isoprenoid_synthase_dom.
    [Graphical view]
    SUPFAMiSSF48576. SSF48576. 1 hit.
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 90 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 (Ref. 3 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

    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.