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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

    Pathway:i3',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)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi165 – 1651MagnesiumBy similarity
    Sitei170 – 1701Transition state stabilizerSequence Analysis
    Binding sitei173 – 1731SubstrateBy similarity
    Binding sitei182 – 1821SubstrateBy similarity
    Active sitei208 – 2081Proton acceptorSequence Analysis
    Metal bindingi208 – 2081MagnesiumBy similarity

    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
    • metabolic process Source: GOC
    • 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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi206 – 2072GG → AA: Cells overexpressing this mutant are no longer swimming suppressed. 1 Publication
    Mutagenesisi208 – 2081E → Q: Significantly decreased biofilm formation. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 296296Diguanylate cyclase YdeHPRO_0000168946Add
    BLAST

    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

    DIPiDIP-11677N.
    IntActiP31129. 6 interactions.
    STRINGi511145.b1535.

    Structurei

    Secondary structure

    1
    296
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 3530Combined sources
    Helixi41 – 444Combined sources
    Helixi48 – 503Combined sources
    Helixi53 – 597Combined sources
    Turni66 – 683Combined sources
    Helixi69 – 9426Combined sources
    Helixi100 – 12526Combined sources
    Turni133 – 1353Combined sources
    Helixi140 – 15213Combined sources
    Beta strandi157 – 16610Combined sources
    Helixi169 – 1768Combined sources
    Helixi178 – 19417Combined sources
    Beta strandi202 – 2043Combined sources
    Beta strandi206 – 21813Combined sources
    Helixi219 – 23517Combined sources
    Beta strandi238 – 2403Combined sources
    Beta strandi243 – 2453Combined sources
    Beta strandi249 – 2568Combined sources
    Helixi262 – 27817Combined sources
    Beta strandi281 – 2877Combined sources
    Beta strandi293 – 2953Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3T9OX-ray2.20A/B2-126[»]
    3TVKX-ray1.80A127-296[»]
    4H54X-ray3.90A/B2-296[»]
    ProteinModelPortaliP31129.
    SMRiP31129. Positions 5-296.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini157 – 289133GGDEFPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 GGDEF domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG2199.
    HOGENOMiHOG000120785.
    InParanoidiP31129.
    OMAiNCTILIN.
    OrthoDBiEOG6G4VQG.
    PhylomeDBiP31129.

    Family and domain databases

    InterProiIPR025991. Chemoreceptor_zinc-bind_dom.
    IPR000160. GGDEF_dom.
    IPR029787. Nucleotide_cyclase.
    [Graphical view]
    PfamiPF13682. CZB. 1 hit.
    PF00990. 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_CP010445.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74608; AAC74608; b1535.
    BAA18882; BAA18882; BAA18882.
    GeneIDi946075.
    KEGGieco: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_CP010445.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3T9OX-ray2.20A/B2-126[»]
    3TVKX-ray1.80A127-296[»]
    4H54X-ray3.90A/B2-296[»]
    ProteinModelPortaliP31129.
    SMRiP31129. Positions 5-296.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-11677N.
    IntActiP31129. 6 interactions.
    STRINGi511145.b1535.

    Proteomic databases

    PaxDbiP31129.
    PRIDEiP31129.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74608; AAC74608; b1535.
    BAA18882; BAA18882; BAA18882.
    GeneIDi946075.
    KEGGieco:b1535.
    PATRICi32118370. VBIEscCol129921_1605.

    Organism-specific databases

    EchoBASEiEB1596.
    EcoGeneiEG11643. ydeH.

    Phylogenomic databases

    eggNOGiCOG2199.
    HOGENOMiHOG000120785.
    InParanoidiP31129.
    OMAiNCTILIN.
    OrthoDBiEOG6G4VQG.
    PhylomeDBiP31129.

    Enzyme and pathway databases

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

    Miscellaneous databases

    PROiP31129.

    Family and domain databases

    InterProiIPR025991. Chemoreceptor_zinc-bind_dom.
    IPR000160. GGDEF_dom.
    IPR029787. Nucleotide_cyclase.
    [Graphical view]
    PfamiPF13682. CZB. 1 hit.
    PF00990. 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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli."
      Cohen S.P., Haechler H., Levy S.B.
      J. Bacteriol. 175:1484-1492(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly regulating the expression of GGDEF proteins."
      Jonas K., Edwards A.N., Simm R., Romeo T., Romling U., Melefors O.
      Mol. Microbiol. 70:236-257(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROBABLE ENZYME ACTIVITY, MUTAGENESIS OF 206-GLY-GLY-207, DISRUPTION PHENOTYPE, POST-TRANSCRIPTIONAL REGULATION BY CSRA.
      Strain: K12.
    6. "Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli."
      Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R.
      Microbiology 155:1318-1331(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION, RPOS-REPRESSION.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    7. "Second messenger signalling governs Escherichia coli biofilm induction upon ribosomal stress."
      Boehm A., Steiner S., Zaehringer F., Casanova A., Hamburger F., Ritz D., Keck W., Ackermann M., Schirmer T., Jenal U.
      Mol. Microbiol. 72:1500-1516(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN BIOFILM FORMATION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT, MUTAGENESIS OF GLU-208, DISRUPTION PHENOTYPE.
      Strain: K12 / AB400.

    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: July 22, 2015
    This is version 116 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

    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.