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Protein

Diguanylate cyclase DgcZ

Gene

dgcZ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the synthesis of cyclic-di-GMP (c-di-GMP) via the condensation of 2 GTP molecules (PubMed:18713317, PubMed:19460094, PubMed:20582742). May act as a zinc sensor that controls, via c-di-GMP, post-translational events (PubMed:23769666). Overexpression leads to a strong repression of swimming; swimming returnes to normal when residues 206-207 are both mutated to Ala. Overexpression also leads to a reduction in flagellar abundance and a 20-fold increase in c-di-GMP levels in vivo. Required for aminoglycoside-mediated induction of biofilm formation, it also plays a lesser role in biofilm production in response to other classes of translation inhibitors. The c-di-GMP produced by this enzyme up-regulates poly-GlcNAc production as well as the biofilm synthesis protein PgaD, although c-di-GMP is probably not the main inducing principle. C-di-GMP is a second messenger which controls cell surface-associated traits in bacteria (PubMed:19460094).1 Publication3 Publications

Catalytic activityi

2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate.1 Publication2 Publications

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per monomer.1 Publication

Enzyme regulationi

Allosterically regulated by zinc, which seems to regulate the activity of the catalytic GGDEF domains by impeding their mobility and thus preventing productive encounter of the two GTP substrates (PubMed:23769666). Subject to product inhibition by c-di-GMP at a KI of 44 µM (PubMed:19460094).2 Publications

Kineticsi

  1. KM=17 µM for GTP1 Publication

    pH dependencei

    Optimum pH is 7.5.1 Publication

    Pathwayi: 3',5'-cyclic di-GMP biosynthesis

    This protein is involved in the pathway 3',5'-cyclic di-GMP biosynthesis, which is part of Purine metabolism.Curated
    View all proteins of this organism that are known to be involved in the pathway 3',5'-cyclic di-GMP biosynthesis and in Purine metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi22Zinc; via tele nitrogenCombined sources1 Publication1
    Metal bindingi52ZincCombined sources1 Publication1
    Metal bindingi79Zinc; via tele nitrogenCombined sources1 Publication1
    Metal bindingi83Zinc; via tele nitrogenCombined sources1 Publication1
    Metal bindingi165MagnesiumCombined sources1 Publication1
    Metal bindingi166Magnesium; via carbonyl oxygenCombined sources1 Publication1
    Sitei170Transition state stabilizerSequence analysis1
    Binding sitei173Substrate1 Publication1
    Binding sitei178Substrate; via carbonyl oxygen1 Publication1
    Binding sitei182Substrate1 Publication1
    Active sitei208Proton acceptorSequence analysis1
    Metal bindingi208MagnesiumCombined sources1 Publication1
    Binding sitei215Substrate; via carbonyl oxygen1 Publication1
    Binding sitei224Substrate1 Publication1
    Binding sitei228Substrate1 Publication1

    GO - Molecular functioni

    • diguanylate cyclase activity Source: EcoCyc
    • GTP binding Source: UniProtKB-KW
    • identical protein binding Source: IntAct
    • zinc ion binding Source: EcoCyc

    GO - Biological processi

    • cell adhesion involved in single-species biofilm formation Source: EcoCyc
    • metabolic process Source: UniProtKB-KW
    • negative regulation of bacterial-type flagellum assembly Source: EcoCyc
    • negative regulation of cellular component movement Source: EcoCyc
    • positive regulation of single-species biofilm formation on inanimate substrate Source: EcoCyc

    Keywordsi

    Molecular functionAllosteric enzyme, Transferase
    LigandGTP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11643-MONOMER
    MetaCyc:EG11643-MONOMER
    UniPathwayiUPA00599

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diguanylate cyclase DgcZ1 Publication (EC:2.7.7.651 Publication2 Publications)
    Short name:
    DGC1 Publication
    Alternative name(s):
    Zinc-sensory diguanylate cyclase1 Publication
    Gene namesi
    Name:dgcZ2 Publications
    Synonyms:ydeG, ydeH
    Ordered Locus Names:b1535, JW1528
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11643 ydeH

    Subcellular locationi

    GO - Cellular componenti

    • cell pole Source: EcoCyc

    Pathology & Biotechi

    Disruption phenotypei

    A slight increase in motility. No visible effect on curli production (PubMed:18713317). Decreased biofilm formation, very little associated poly-GlcNAc production, and a complete loss of aminoglycoside-mediated induction of biofilm formation (PubMed:19460094).2 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi52C → A: Decreases zinc affinity by one order of magnitude. 1 Publication1
    Mutagenesisi79H → L: Displays constitutively high biofilm and PgaD levels; when associated with L-83. 1 Publication1
    Mutagenesisi83H → L: Displays constitutively high biofilm and PgaD levels; when associated with L-79. 1 Publication1
    Mutagenesisi206 – 207GG → AA: Cells overexpressing this mutant are no longer swimming suppressed. 1 Publication2
    Mutagenesisi208E → Q: Significantly decreased biofilm formation. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001689461 – 296Diguanylate cyclase DgcZAdd BLAST296

    Proteomic databases

    PaxDbiP31129
    PRIDEiP31129

    Expressioni

    Inductioni

    CsrA binds to the mRNA and reduces its levels. Expressed at low levels at both 28 and 37 degrees Celsius. Repressed by RpoS.2 Publications

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    itself3EBI-1124405,EBI-1124405

    GO - Molecular functioni

    • identical protein binding Source: IntAct

    Protein-protein interaction databases

    BioGridi4259114, 10 interactors
    DIPiDIP-11677N
    IntActiP31129, 6 interactors
    STRINGi316385.ECDH10B_1666

    Structurei

    Secondary structure

    1296
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 35Combined sources30
    Helixi41 – 44Combined sources4
    Helixi48 – 50Combined sources3
    Helixi53 – 59Combined sources7
    Turni66 – 68Combined sources3
    Helixi69 – 94Combined sources26
    Helixi100 – 125Combined sources26
    Turni133 – 135Combined sources3
    Helixi140 – 152Combined sources13
    Beta strandi157 – 166Combined sources10
    Helixi169 – 176Combined sources8
    Helixi178 – 194Combined sources17
    Beta strandi202 – 204Combined sources3
    Beta strandi206 – 218Combined sources13
    Helixi219 – 235Combined sources17
    Beta strandi238 – 240Combined sources3
    Beta strandi243 – 245Combined sources3
    Beta strandi249 – 256Combined sources8
    Helixi262 – 278Combined sources17
    Beta strandi281 – 287Combined sources7
    Beta strandi293 – 295Combined sources3

    3D structure databases

    ProteinModelPortaliP31129
    SMRiP31129
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini157 – 289GGDEFPROSITE-ProRule annotationAdd BLAST133

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni195 – 200Substrate binding1 Publication6

    Domaini

    Contains an N-terminal CZB (chemoreceptor zinc binding) domain and a C-terminal GGDEF domain.1 Publication

    Phylogenomic databases

    eggNOGiENOG4105FSR Bacteria
    COG2199 LUCA
    HOGENOMiHOG000120785
    InParanoidiP31129
    KOiK13069
    OMAiNCTILIN
    PhylomeDBiP31129

    Family and domain databases

    CDDicd01949 GGDEF, 1 hit
    InterProiView protein in InterPro
    IPR000160 GGDEF_dom
    IPR029787 Nucleotide_cyclase
    PfamiView protein in Pfam
    PF00990 GGDEF, 1 hit
    SMARTiView protein in SMART
    SM00267 GGDEF, 1 hit
    SUPFAMiSSF55073 SSF55073, 1 hit
    TIGRFAMsiTIGR00254 GGDEF, 1 hit
    PROSITEiView protein in PROSITE
    PS50887 GGDEF, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P31129-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MIKKTTEIDA ILLNLNKAID AHYQWLVSMF HSVVARDASK PEITDNHSYG
    60 70 80 90 100
    LCQFGRWIDH LGPLDNDELP YVRLMDSAHQ HMHNCGRELM LAIVENHWQD
    110 120 130 140 150
    AHFDAFQEGL LSFTAALTDY KIYLLTIRSN MDVLTGLPGR RVLDESFDHQ
    160 170 180 190 200
    LRNAEPLNLY LMLLDIDRFK LVNDTYGHLI GDVVLRTLAT YLASWTRDYE
    210 220 230 240 250
    TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH SEGHINITVT
    260 270 280 290
    AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV
    Length:296
    Mass (Da):33,863
    Last modified:July 15, 1998 - v2
    Checksum:i7B6884E6B8A6D8D8
    GO

    Sequence cautioni

    The sequence M96235 differs from that shown. Reason: Frameshift at position 176.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M96235 Genomic DNA No translation available.
    U00096 Genomic DNA Translation: AAC74608.1
    AP009048 Genomic DNA Translation: BAA18882.2
    PIRiB64908
    RefSeqiNP_416052.1, NC_000913.3
    WP_000592814.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC74608; AAC74608; b1535
    BAA18882; BAA18882; BAA18882
    GeneIDi946075
    KEGGiecj:JW1528
    eco:b1535
    PATRICifig|511145.12.peg.1605

    Similar proteinsi

    Entry informationi

    Entry nameiDGCZ_ECOLI
    AccessioniPrimary (citable) accession number: P31129
    Secondary accession number(s): P76152, P77452
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
    Last sequence update: July 15, 1998
    Last modified: July 18, 2018
    This is version 133 of the entry and version 2 of the sequence. See 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

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