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Protein

Diguanylate cyclase YdeH

Gene

ydeH

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

A diguanylate cyclase, 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. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.1 Publication

Catalytic activityi

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

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per monomer.By similarity

Enzyme regulationi

Subject to product inhibition by c-di-GMP at a KI of 44 µM.1 Publication

Kineticsi

  1. KM=17 µM for GTP1 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.
    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 bindingi165MagnesiumBy similarity1
    Sitei170Transition state stabilizerSequence analysis1
    Binding sitei173SubstrateBy similarity1
    Binding sitei182SubstrateBy similarity1
    Active sitei208Proton acceptorSequence analysis1
    Metal bindingi208MagnesiumBy similarity1

    GO - Molecular functioni

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

    GO - Biological processi

    • cell adhesion involved in single-species biofilm formation Source: EcoCyc
    • negative regulation of bacterial-type flagellum assembly Source: EcoCyc
    • negative regulation of cellular component movement Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Transferase

    Keywords - Ligandi

    GTP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11643-MONOMER.
    ECOL316407:JW1528-MONOMER.
    MetaCyc:EG11643-MONOMER.
    UniPathwayiUPA00599.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diguanylate cyclase YdeH (EC:2.7.7.65)
    Short name:
    DGC
    Gene namesi
    Name:ydeH
    Synonyms:ydeG
    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.

    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
    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 YdeHAdd 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.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi4259114. 9 interactors.
    DIPiDIP-11677N.
    IntActiP31129. 6 interactors.
    STRINGi511145.b1535.

    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

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3T9OX-ray2.20A/B2-126[»]
    3TVKX-ray1.80A127-296[»]
    4H54X-ray3.90A/B2-296[»]
    ProteinModelPortaliP31129.
    SMRiP31129.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

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

    Sequence similaritiesi

    Contains 1 GGDEF domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiENOG4105FSR. Bacteria.
    COG2199. LUCA.
    HOGENOMiHOG000120785.
    InParanoidiP31129.
    KOiK13069.
    OMAiNCTILIN.
    PhylomeDBiP31129.

    Family and domain databases

    CDDicd01949. GGDEF. 1 hit.
    InterProiIPR000160. GGDEF_dom.
    IPR029787. Nucleotide_cyclase.
    [Graphical view]
    PfamiPF00990. GGDEF. 1 hit.
    [Graphical view]
    SMARTiSM00267. GGDEF. 1 hit.
    [Graphical view]
    SUPFAMiSSF55073. SSF55073. 1 hit.
    TIGRFAMsiTIGR00254. GGDEF. 1 hit.
    PROSITEiPS50887. GGDEF. 1 hit.
    [Graphical view]

    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.
    PATRICi32118370. VBIEscCol129921_1605.

    Cross-referencesi

    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3T9OX-ray2.20A/B2-126[»]
    3TVKX-ray1.80A127-296[»]
    4H54X-ray3.90A/B2-296[»]
    ProteinModelPortaliP31129.
    SMRiP31129.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259114. 9 interactors.
    DIPiDIP-11677N.
    IntActiP31129. 6 interactors.
    STRINGi511145.b1535.

    Proteomic databases

    PaxDbiP31129.
    PRIDEiP31129.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74608; AAC74608; b1535.
    BAA18882; BAA18882; BAA18882.
    GeneIDi946075.
    KEGGiecj:JW1528.
    eco:b1535.
    PATRICi32118370. VBIEscCol129921_1605.

    Organism-specific databases

    EchoBASEiEB1596.
    EcoGeneiEG11643. ydeH.

    Phylogenomic databases

    eggNOGiENOG4105FSR. Bacteria.
    COG2199. LUCA.
    HOGENOMiHOG000120785.
    InParanoidiP31129.
    KOiK13069.
    OMAiNCTILIN.
    PhylomeDBiP31129.

    Enzyme and pathway databases

    UniPathwayiUPA00599.
    BioCyciEcoCyc:EG11643-MONOMER.
    ECOL316407:JW1528-MONOMER.
    MetaCyc:EG11643-MONOMER.

    Miscellaneous databases

    PROiP31129.

    Family and domain databases

    CDDicd01949. GGDEF. 1 hit.
    InterProiIPR000160. GGDEF_dom.
    IPR029787. Nucleotide_cyclase.
    [Graphical view]
    PfamiPF00990. GGDEF. 1 hit.
    [Graphical view]
    SMARTiSM00267. GGDEF. 1 hit.
    [Graphical view]
    SUPFAMiSSF55073. SSF55073. 1 hit.
    TIGRFAMsiTIGR00254. GGDEF. 1 hit.
    PROSITEiPS50887. GGDEF. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiYDEH_ECOLI
    AccessioniPrimary (citable) accession number: P31129
    Secondary accession number(s): P76152, P77452
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 1993
    Last sequence update: July 15, 1998
    Last modified: November 2, 2016
    This is version 124 of the entry and version 2 of the sequence. [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
    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.