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P31129

- YDEH_ECOLI

UniProt

P31129 - YDEH_ECOLI

Protein

Diguanylate cyclase YdeH

Gene

ydeH

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 109 (01 Oct 2014)
      Sequence version 2 (15 Jul 1998)
      Previous versions | rss
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    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

    Binds 1 Mg2+ 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

    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

    1. diguanylate cyclase activity Source: EcoCyc
    2. GTP binding Source: UniProtKB-KW
    3. phosphorus-oxygen lyase activity Source: InterPro
    4. zinc ion binding Source: EcoCyc

    GO - Biological processi

    1. cell adhesion involved in single-species biofilm formation Source: EcoCyc
    2. cyclic nucleotide biosynthetic process Source: InterPro
    3. intracellular signal transduction Source: InterPro
    4. negative regulation of bacterial-type flagellum assembly Source: EcoCyc
    5. negative regulation of cellular component movement Source: EcoCyc

    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: Chromosome, UP000000625: 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 aminogylcoside-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. 2 Publications

    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

    Gene expression databases

    GenevestigatoriP31129.

    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 – 3530
    Helixi53 – 597
    Turni66 – 683
    Helixi69 – 9426
    Helixi100 – 12526
    Turni133 – 1353
    Helixi140 – 15213
    Beta strandi157 – 16610
    Helixi169 – 1768
    Helixi178 – 19417
    Beta strandi202 – 2043
    Beta strandi206 – 21813
    Helixi219 – 23517
    Beta strandi238 – 2403
    Beta strandi243 – 2453
    Beta strandi249 – 2568
    Helixi262 – 27817
    Beta strandi281 – 2877
    Beta strandi293 – 2953

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    OMAiNCTILIN.
    OrthoDBiEOG6G4VQG.
    PhylomeDBiP31129.

    Family and domain databases

    InterProiIPR001054. A/G_cyclase.
    IPR025991. Chemoreceptor_zinc-bind_dom.
    IPR000160. GGDEF_dom.
    [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

    MIKKTTEIDA ILLNLNKAID AHYQWLVSMF HSVVARDASK PEITDNHSYG    50
    LCQFGRWIDH LGPLDNDELP YVRLMDSAHQ HMHNCGRELM LAIVENHWQD 100
    AHFDAFQEGL LSFTAALTDY KIYLLTIRSN MDVLTGLPGR RVLDESFDHQ 150
    LRNAEPLNLY LMLLDIDRFK LVNDTYGHLI GDVVLRTLAT YLASWTRDYE 200
    TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH SEGHINITVT 250
    AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV 296
    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.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    YP_489798.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74608; AAC74608; b1535.
    BAA18882; BAA18882; BAA18882.
    GeneIDi12930120.
    946075.
    KEGGiecj:Y75_p1510.
    eco:b1535.
    PATRICi32118370. VBIEscCol129921_1605.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M96235 Genomic DNA. No translation available.
    U00096 Genomic DNA. Translation: AAC74608.1 .
    AP009048 Genomic DNA. Translation: BAA18882.2 .
    PIRi B64908.
    RefSeqi NP_416052.1. NC_000913.3.
    YP_489798.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3T9O X-ray 2.20 A/B 2-126 [» ]
    3TVK X-ray 1.80 A 127-296 [» ]
    4H54 X-ray 3.90 A/B 2-296 [» ]
    ProteinModelPortali P31129.
    SMRi P31129. Positions 5-296.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-11677N.
    IntActi P31129. 6 interactions.
    STRINGi 511145.b1535.

    Proteomic databases

    PaxDbi P31129.
    PRIDEi P31129.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74608 ; AAC74608 ; b1535 .
    BAA18882 ; BAA18882 ; BAA18882 .
    GeneIDi 12930120.
    946075.
    KEGGi ecj:Y75_p1510.
    eco:b1535.
    PATRICi 32118370. VBIEscCol129921_1605.

    Organism-specific databases

    EchoBASEi EB1596.
    EcoGenei EG11643. ydeH.

    Phylogenomic databases

    eggNOGi COG2199.
    HOGENOMi HOG000120785.
    OMAi NCTILIN.
    OrthoDBi EOG6G4VQG.
    PhylomeDBi P31129.

    Enzyme and pathway databases

    UniPathwayi UPA00599 .
    BioCyci EcoCyc:EG11643-MONOMER.
    ECOL316407:JW1528-MONOMER.
    MetaCyc:EG11643-MONOMER.

    Miscellaneous databases

    PROi P31129.

    Gene expression databases

    Genevestigatori P31129.

    Family and domain databases

    InterProi IPR001054. A/G_cyclase.
    IPR025991. Chemoreceptor_zinc-bind_dom.
    IPR000160. GGDEF_dom.
    [Graphical view ]
    Pfami PF13682. CZB. 1 hit.
    PF00990. GGDEF. 1 hit.
    [Graphical view ]
    SMARTi SM00267. GGDEF. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55073. SSF55073. 1 hit.
    TIGRFAMsi TIGR00254. GGDEF. 1 hit.
    PROSITEi PS50887. GGDEF. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 109 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