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P31129

- YDEH_ECOLI

UniProt

P31129 - YDEH_ECOLI

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Protein

Diguanylate cyclase YdeH

Gene

ydeH

Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

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. zinc ion binding Source: EcoCyc

GO - Biological processi

  1. cell adhesion involved in single-species biofilm formation Source: EcoCyc
  2. metabolic process Source: GOC
  3. negative regulation of bacterial-type flagellum assembly Source: EcoCyc
  4. 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: 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. 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

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.
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.

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.
InParanoidi P31129.
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 IPR025991. Chemoreceptor_zinc-bind_dom.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
[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

« 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: October 29, 2014
This is version 110 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