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P31129 (YDEH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Diguanylate cyclase YdeH

Short name=DGC
EC=2.7.7.65
Gene names
Name:ydeH
Synonyms:ydeG
Ordered Locus Names:b1535, JW1528
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length296 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.7

Catalytic activity

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

Cofactor

Binds 1 Mg2+ per monomer By similarity.

Enzyme regulation

Subject to product inhibition by c-di-GMP at a KI of 44 µM. Ref.7

Pathway

Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.

Subunit structure

Homodimer. Ref.7

Induction

CsrA binds to the mRNA and reduces its levels. Expressed at low levels at both 28 and 37 degrees Celsius. Repressed by RpoS. Ref.5 Ref.6 Ref.7

Disruption phenotype

A slight increase in motility. No visible effect on curli production (Ref.5). Decreased biofilm formation, very little associated poly-GlcNAc production, and a complete loss of aminogylcoside-mediated induction of biofilm formation (Ref.7). Ref.5 Ref.7

Sequence similarities

Contains 1 GGDEF domain.

Biophysicochemical properties

Kinetic parameters:

KM=17 µM for GTP Ref.7

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 296296Diguanylate cyclase YdeH
PRO_0000168946

Regions

Domain157 – 289133GGDEF

Sites

Active site2081Proton acceptor Potential
Metal binding1651Magnesium By similarity
Metal binding2081Magnesium By similarity
Binding site1731Substrate By similarity
Binding site1821Substrate By similarity
Site1701Transition state stabilizer Potential

Experimental info

Mutagenesis206 – 2072GG → AA: Cells overexpressing this mutant are no longer swimming suppressed. Ref.5
Mutagenesis2081E → Q: Significantly decreased biofilm formation. Ref.5 Ref.7

Secondary structure

..................................... 296
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P31129 [UniParc].

Last modified July 15, 1998. Version 2.
Checksum: 7B6884E6B8A6D8D8

FASTA29633,863
        10         20         30         40         50         60 
MIKKTTEIDA ILLNLNKAID AHYQWLVSMF HSVVARDASK PEITDNHSYG LCQFGRWIDH 

        70         80         90        100        110        120 
LGPLDNDELP YVRLMDSAHQ HMHNCGRELM LAIVENHWQD AHFDAFQEGL LSFTAALTDY 

       130        140        150        160        170        180 
KIYLLTIRSN MDVLTGLPGR RVLDESFDHQ LRNAEPLNLY LMLLDIDRFK LVNDTYGHLI 

       190        200        210        220        230        240 
GDVVLRTLAT YLASWTRDYE TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH 

       250        260        270        280        290 
SEGHINITVT AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV 

« Hide

References

« Hide 'large scale' references
[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]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M96235 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC74608.1.
AP009048 Genomic DNA. Translation: BAA18882.2.
PIRB64908.
RefSeqNP_416052.1. NC_000913.3.
YP_489798.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3T9OX-ray2.20A/B2-126[»]
3TVKX-ray1.80A127-296[»]
4H54X-ray3.90A/B2-296[»]
ProteinModelPortalP31129.
SMRP31129. Positions 5-296.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-11677N.
IntActP31129. 6 interactions.
STRING511145.b1535.

Proteomic databases

PaxDbP31129.
PRIDEP31129.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74608; AAC74608; b1535.
BAA18882; BAA18882; BAA18882.
GeneID12930120.
946075.
KEGGecj:Y75_p1510.
eco:b1535.
PATRIC32118370. VBIEscCol129921_1605.

Organism-specific databases

EchoBASEEB1596.
EcoGeneEG11643. ydeH.

Phylogenomic databases

eggNOGCOG2199.
HOGENOMHOG000120785.
OMANCTILIN.
OrthoDBEOG6G4VQG.
PhylomeDBP31129.

Enzyme and pathway databases

BioCycEcoCyc:EG11643-MONOMER.
ECOL316407:JW1528-MONOMER.
MetaCyc:EG11643-MONOMER.
UniPathwayUPA00599.

Gene expression databases

GenevestigatorP31129.

Family and domain databases

InterProIPR001054. A/G_cyclase.
IPR025991. Chemoreceptor_zinc-bind_dom.
IPR000160. GGDEF_dom.
[Graphical view]
PfamPF13682. CZB. 1 hit.
PF00990. GGDEF. 1 hit.
[Graphical view]
SMARTSM00267. GGDEF. 1 hit.
[Graphical view]
SUPFAMSSF55073. SSF55073. 1 hit.
TIGRFAMsTIGR00254. GGDEF. 1 hit.
PROSITEPS50887. GGDEF. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROP31129.

Entry information

Entry nameYDEH_ECOLI
AccessionPrimary (citable) accession number: P31129
Secondary accession number(s): P76152, P77452
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 15, 1998
Last modified: May 14, 2014
This is version 108 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene