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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. Fe2+ or Cu2+ ions are very less efficient as cofactors.2 Publications

Kineticsi

  1. KM=62 nM for FPP1 Publication

    Pathwayi: geosmin 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.

    Pathwayi: germacradienol 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.

    Pathwayi: germacrene 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)DescriptionActionsGraphical viewLength
    Metal bindingi86MagnesiumSequence analysis1
    Metal bindingi91MagnesiumSequence analysis1
    Metal bindingi267MagnesiumSequence analysis1
    Metal bindingi271MagnesiumSequence analysis1
    Metal bindingi276MagnesiumSequence analysis1
    Metal bindingi455MagnesiumSequence analysis1
    Metal bindingi598MagnesiumSequence analysis1
    Metal bindingi602MagnesiumSequence analysis1
    Metal bindingi606MagnesiumSequence analysis1

    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
    Proteomesi
    • UP000001973 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00002478952 – 726Germacradienol/geosmin synthaseAdd BLAST725

    Proteomic databases

    PRIDEiQ9X839.

    Interactioni

    Protein-protein interaction databases

    STRINGi100226.SCO6073.

    Structurei

    Secondary structure

    1726
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi23 – 37Combined sources15
    Beta strandi43 – 45Combined sources3
    Helixi48 – 54Combined sources7
    Helixi56 – 63Combined sources8
    Helixi69 – 92Combined sources24
    Turni93 – 97Combined sources5
    Helixi99 – 108Combined sources10
    Helixi109 – 112Combined sources4
    Helixi127 – 139Combined sources13
    Helixi140 – 142Combined sources3
    Helixi145 – 171Combined sources27
    Helixi177 – 187Combined sources11
    Helixi190 – 200Combined sources11
    Helixi206 – 209Combined sources4
    Helixi212 – 239Combined sources28
    Helixi247 – 255Combined sources9
    Helixi259 – 282Combined sources24
    Helixi284 – 291Combined sources8
    Helixi296 – 320Combined sources25
    Helixi324 – 326Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    5DW7X-ray3.20A1-366[»]
    5DZ2X-ray2.11A/B1-338[»]
    ProteinModelPortaliQ9X839.
    SMRiQ9X839.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni2 – 354Germacradienol/germacrene D synthaseAdd BLAST353
    Regioni355 – 726Geosmin synthaseAdd BLAST372

    Motif

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Motifi86 – 91DDXXD motif 1; degenerate6
    Motifi455 – 459DDXXD motif 2; degenerate5

    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

    eggNOGiENOG4105IK6. Bacteria.
    ENOG410XSNU. LUCA.
    HOGENOMiHOG000253477.
    InParanoidiQ9X839.
    KOiK10187.
    OMAiIEMRRKV.
    OrthoDBiPOG091H0EGW.

    Family and domain databases

    Gene3Di1.10.600.10. 2 hits.
    InterProiIPR008949. Isoprenoid_synthase_dom.
    [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

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    5DW7X-ray3.20A1-366[»]
    5DZ2X-ray2.11A/B1-338[»]
    ProteinModelPortaliQ9X839.
    SMRiQ9X839.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi100226.SCO6073.

    Proteomic databases

    PRIDEiQ9X839.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Phylogenomic databases

    eggNOGiENOG4105IK6. Bacteria.
    ENOG410XSNU. LUCA.
    HOGENOMiHOG000253477.
    InParanoidiQ9X839.
    KOiK10187.
    OMAiIEMRRKV.
    OrthoDBiPOG091H0EGW.

    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.
    [Graphical view]
    SUPFAMiSSF48576. SSF48576. 2 hits.
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 99 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

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Protein Spotlight
      Protein Spotlight articles and cited UniProtKB/Swiss-Prot entries
    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.