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Protein

Germacradienol/geosmin synthase

Gene

cyc2

Organism
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Tow-domain protein where the N-terminal domain catalyzes the cyclization of farnesyl diphosphate (FPP) to a 85:15 mixture of the sesquiterpene alcohol germacradienol and the sesquiterpene hydrocarbon germacrene D. The C-terminal domain partially converts the germacradienol formed into geosmin, the characteristic odoriferous ('earthy aroma') constituent of Streptomyces species.4 Publications

Catalytic activityi

(2E,6E)-farnesyl diphosphate + H2O = (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + diphosphate.1 Publication
(1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O = (-)-geosmin + acetone.1 Publication
(2E,6E)-farnesyl diphosphate = (-)-germacrene D + diphosphate.1 Publication

Cofactori

Mg2+2 PublicationsNote: Magnesium. Fe(2+) or Cu2+ ions are very less efficient as cofactors.2 Publications

Kineticsi

  1. KM=62 nM for FPP1 Publication

    Pathway:igeosmin biosynthesis

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

    Pathway:igermacradienol biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes germacradienol from farnesyl diphosphate.
    Proteins known to be involved in this subpathway in this organism are:
    1. Germacradienol/geosmin synthase (cyc2)
    This subpathway is part of the pathway germacradienol 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 germacradienol from farnesyl diphosphate, the pathway germacradienol biosynthesis and in Sesquiterpene biosynthesis.

    Pathway:igermacrene D biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes germacrene D from farnesyl diphosphate.
    Proteins known to be involved in this subpathway in this organism are:
    1. Germacradienol/geosmin synthase (cyc2)
    This subpathway is part of the pathway germacrene D 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 germacrene D from farnesyl diphosphate, the pathway germacrene D biosynthesis and in Sesquiterpene biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi86 – 861MagnesiumSequence Analysis
    Metal bindingi91 – 911MagnesiumSequence Analysis
    Metal bindingi267 – 2671MagnesiumSequence Analysis
    Metal bindingi271 – 2711MagnesiumSequence Analysis
    Metal bindingi276 – 2761MagnesiumSequence Analysis
    Metal bindingi455 – 4551MagnesiumSequence Analysis
    Metal bindingi598 – 5981MagnesiumSequence Analysis
    Metal bindingi602 – 6021MagnesiumSequence Analysis
    Metal bindingi606 – 6061MagnesiumSequence Analysis

    GO - Molecular functioni

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-14022.
    BRENDAi4.1.99.16. 5998.
    4.2.3.22. 5998.
    SABIO-RKQ9X839.
    UniPathwayiUPA00209.
    UPA00283; UER00583.
    UPA00285; UER00584.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Germacradienol/geosmin synthase
    Including the following 2 domains:
    Germacradienol/germacrene D synthase (EC:4.2.3.22, EC:4.2.3.75)
    Alternative name(s):
    Sesquiterpene cyclase
    Sesquiterpene synthase
    Geosmin synthase (EC:4.1.99.16)
    Gene namesi
    Name:cyc2
    Ordered Locus Names:SCO6073
    ORF Names:SC9B1.20
    OrganismiStreptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
    Taxonomic identifieri100226 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomycesStreptomyces albidoflavus group
    ProteomesiUP000001973 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 726725Germacradienol/geosmin synthasePRO_0000247895Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi100226.SCO6073.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9X839.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni2 – 354353Germacradienol/germacrene D synthaseAdd
    BLAST
    Regioni355 – 726372Geosmin synthaseAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi86 – 916DDXXD motif 1; degenerate
    Motifi455 – 4595DDXXD motif 2; degenerate

    Domaini

    Consists of 2 homologous sesquiterpene synthase domains. The Asp-Asp-Xaa-Xaa-Asp/Glu (DDXXD/E) motif is important for the catalytic activity, presumably through binding to Mg2+.2 Publications

    Sequence similaritiesi

    Belongs to the terpene synthase family.Curated

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiNOG15313.
    HOGENOMiHOG000253477.
    InParanoidiQ9X839.
    KOiK10187.
    OMAiIEMRRKV.
    OrthoDBiEOG622PK5.

    Family and domain databases

    Gene3Di1.10.600.10. 2 hits.
    InterProiIPR008949. Isoprenoid_synthase_dom.
    IPR005630. Terpene_synthase_metal-bd.
    [Graphical view]
    PfamiPF03936. Terpene_synth_C. 2 hits.
    [Graphical view]
    SUPFAMiSSF48576. SSF48576. 2 hits.

    Sequencei

    Sequence statusi: Complete.

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

    Q9X839-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTQQPFQLPH FYLPHPARLN PHLDEARAHS TTWAREMGML EGSGVWEQSD
    60 70 80 90 100
    LEAHDYGLLC AYTHPDCDGP ALSLITDWYV WVFFFDDHFL EKYKRSQDRL
    110 120 130 140 150
    AGKAHLDRLP LFMPLDDAAG MPEPRNPVEA GLADLWTRTV PAMSADWRRR
    160 170 180 190 200
    FAVATEHLLN ESMWELSNIN EGRVANPVEY IEMRRKVGGA PWSAGLVEYA
    210 220 230 240 250
    TAEVPAAVAG TRPLRVLMET FSDAVHLRND LFSYQREVED EGELSNGVLV
    260 270 280 290 300
    LETFFGCTTQ EAADLVNDVL TSRLHQFEHT AFTEVPAVAL EKGLTPLEVA
    310 320 330 340 350
    AVGAYTKGLQ DWQSGGHEWH MRSSRYMNKG ERPLAGWQAL TGPGTSAADV
    360 370 380 390 400
    GALLADAVAQ RARSYTYVPF QKVGPSVIPD IRMPYPLELS PALDGARRHL
    410 420 430 440 450
    SEWCREMGIL SEGVWDEDKL ESCDLPLCAA GLDPDATQDQ LDLASGWLAF
    460 470 480 490 500
    GTYGDDYYPL VYGHRRDLAA ARLTTTRLSD CMPLDGEPVP PPGNAMERSL
    510 520 530 540 550
    IDLWVRTTAG MTPEERRPLK KAVDDMTEAW LWELSNQIQN RVPDPVDYLE
    560 570 580 590 600
    MRRATFGSDL TLGLCRAGHG PAVPPEVYRS GPVRSLENAA IDYACLLNDV
    610 620 630 640 650
    FSYQKEIEYE GEIHNAVLVV QNFFGVDYPA ALGVVQDLMN QRMRQFEHVV
    660 670 680 690 700
    AHELPVVYDD FQLSEEARTV MRGYVTDLQN WMAGILNWHR NVPRYKAEYL
    710 720
    AGRTHGFLPD RIPAPPVPRS SPALTH
    Length:726
    Mass (Da):81,474
    Last modified:January 23, 2007 - v3
    Checksum:iCB332AC7840EB81E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL939126 Genomic DNA. Translation: CAB41566.1.
    PIRiT35865.
    RefSeqiNP_630182.1. NC_003888.3.
    WP_011030632.1. NC_003888.3.

    Genome annotation databases

    EnsemblBacteriaiCAB41566; CAB41566; CAB41566.
    GeneIDi1101514.
    KEGGisco:SCO6073.
    PATRICi23742056. VBIStrCoe124346_6175.

    Cross-referencesi

    Web resourcesi

    Protein Spotlight

    The earth's perfume - Issue 35 of June 2003

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL939126 Genomic DNA. Translation: CAB41566.1.
    PIRiT35865.
    RefSeqiNP_630182.1. NC_003888.3.
    WP_011030632.1. NC_003888.3.

    3D structure databases

    ProteinModelPortaliQ9X839.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi100226.SCO6073.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB41566; CAB41566; CAB41566.
    GeneIDi1101514.
    KEGGisco:SCO6073.
    PATRICi23742056. VBIStrCoe124346_6175.

    Phylogenomic databases

    eggNOGiNOG15313.
    HOGENOMiHOG000253477.
    InParanoidiQ9X839.
    KOiK10187.
    OMAiIEMRRKV.
    OrthoDBiEOG622PK5.

    Enzyme and pathway databases

    UniPathwayiUPA00209.
    UPA00283; UER00583.
    UPA00285; UER00584.
    BioCyciMetaCyc:MONOMER-14022.
    BRENDAi4.1.99.16. 5998.
    4.2.3.22. 5998.
    SABIO-RKQ9X839.

    Family and domain databases

    Gene3Di1.10.600.10. 2 hits.
    InterProiIPR008949. Isoprenoid_synthase_dom.
    IPR005630. Terpene_synthase_metal-bd.
    [Graphical view]
    PfamiPF03936. Terpene_synth_C. 2 hits.
    [Graphical view]
    SUPFAMiSSF48576. SSF48576. 2 hits.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-471 / A3(2) / M145.
    2. "Expression and mechanistic analysis of a germacradienol synthase from Streptomyces coelicolor implicated in geosmin biosynthesis."
      Cane D.E., Watt R.M.
      Proc. Natl. Acad. Sci. U.S.A. 100:1547-1551(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-10, FUNCTION, CATALYTIC ACTIVITY, DOMAIN, KINETIC PARAMETERS, COFACTOR.
      Strain: ATCC BAA-471 / A3(2) / M145.
    3. "PCR-targeted Streptomyces gene replacement identifies a protein domain needed for biosynthesis of the sesquiterpene soil odor geosmin."
      Gust B., Challis G.L., Fowler K., Kieser T., Chater K.F.
      Proc. Natl. Acad. Sci. U.S.A. 100:1541-1546(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: DOMAIN, ROLE IN GEOSMIN BIOSYNTHESIS.
      Strain: ATCC BAA-471 / A3(2) / M145.
    4. "Mechanism and stereochemistry of the germacradienol/germacrene D synthase of Streptomyces coelicolor A3(2)."
      He X., Cane D.E.
      J. Am. Chem. Soc. 126:2678-2679(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN GERMACRENE D PRODUCTION, REACTION STEREOCHEMISTRY.
      Strain: ATCC BAA-471 / A3(2) / M145.
    5. "Geosmin biosynthesis. Streptomyces coelicolor germacradienol/germacrene D synthase converts farnesyl diphosphate to geosmin."
      Jiang J., He X., Cane D.E.
      J. Am. Chem. Soc. 128:8128-8129(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN DIRECT GEOSMIN PRODUCTION, COFACTOR, REACTION MECHANISM.
      Strain: ATCC BAA-471 / A3(2) / M145.

    Entry informationi

    Entry nameiCYC2_STRCO
    AccessioniPrimary (citable) accession number: Q9X839
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 25, 2006
    Last sequence update: January 23, 2007
    Last modified: June 24, 2015
    This is version 91 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The earthy odorant geosmin is also responsible for the 'off-flavor' of contaminated drinking water, wines, and other foodstuffs.

    Caution

    It is uncertain whether the initial Met is cleaved or not.Curated

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. Protein Spotlight
      Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.