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Protein

Probable diguanylate cyclase YdaM

Gene

ydaM

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

Functioni

Part of a 2 protein system that seems to be dedicated to regulate transcription of csgD. The CsdG protein in turn regulates expression of adhesive curli fimbriae genes csgEFG, csgBAC/ymaD and adrA (yaic). Activity of this protein is antagonized by the phosphodiesterase Gmr (YciR). In vitro has weak diguanylate cyclase activity. 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.1 Publication

Cofactori

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

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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi291 – 2911MagnesiumBy similarity
Sitei296 – 2961Transition state stabilizerSequence analysis
Binding sitei299 – 2991SubstrateBy similarity
Binding sitei308 – 3081SubstrateBy similarity
Active sitei334 – 3341Proton acceptorSequence analysis
Metal bindingi334 – 3341MagnesiumBy similarity

GO - Molecular functioni

  • diguanylate cyclase activity Source: EcoCyc
  • GTP binding Source: UniProtKB-KW
  • identical protein binding Source: IntAct
  • metal ion binding Source: UniProtKB-KW
  • phosphorelay sensor kinase activity Source: InterPro

GO - Biological processi

  • positive regulation of sequence-specific DNA binding transcription factor activity Source: EcoCyc
  • positive regulation of single-species biofilm formation on inanimate substrate Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciEcoCyc:G6673-MONOMER.
ECOL316407:JW5206-MONOMER.
MetaCyc:G6673-MONOMER.
UniPathwayiUPA00599.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable diguanylate cyclase YdaM (EC:2.7.7.65)
Short name:
DGC
Gene namesi
Name:ydaM
Ordered Locus Names:b1341, JW5206
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13355. ydaM.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Loss of curli fimbriae, decreased biofilm formation, decreased expression of AdrA, a probable diguanylate cyclase and of the curli regulator CsgD.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi334 – 3352EE → AA: No longer complements a ydaM disruption, loss of csgB induction. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 410410Probable diguanylate cyclase YdaMPRO_0000201313Add
BLAST

Proteomic databases

PaxDbiP77302.

Expressioni

Inductioni

Expressed during transition into stationary phase, expression is higher at 28 than 37 degrees Celsius, more highly expressed on plates than in liquid medium. In rich medium YdaM and DosC are the major RpoS-dependent GGDEF-domain containing proteins in the cell. Expression is RpoS and HNS dependent.2 Publications

Interactioni

Subunit structurei

Homodimer.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-544662,EBI-544662
gmrP773345EBI-544662,EBI-548149
mlrAP333582EBI-544662,EBI-1127668

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi4259650. 11 interactions.
DIPiDIP-28053N.
IntActiP77302. 6 interactions.
STRINGi511145.b1341.

Structurei

3D structure databases

ProteinModelPortaliP77302.
SMRiP77302. Positions 256-407.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 7068PAS 1Add
BLAST
Domaini129 – 19870PAS 2Add
BLAST
Domaini199 – 25153PACPROSITE-ProRule annotationAdd
BLAST
Domaini283 – 410128GGDEFPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 GGDEF domain.PROSITE-ProRule annotation
Contains 1 PAC (PAS-associated C-terminal) domain.PROSITE-ProRule annotation
Contains 2 PAS (PER-ARNT-SIM) domains.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
COG2199. LUCA.
COG2202. LUCA.
HOGENOMiHOG000120131.
InParanoidiP77302.
OMAiKLMLCII.
PhylomeDBiP77302.

Family and domain databases

CDDicd01949. GGDEF. 1 hit.
InterProiIPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR000014. PAS.
IPR000700. PAS-assoc_C.
IPR013656. PAS_4.
[Graphical view]
PfamiPF00990. GGDEF. 1 hit.
PF08448. PAS_4. 1 hit.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
SM00091. PAS. 2 hits.
[Graphical view]
SUPFAMiSSF55073. SSF55073. 1 hit.
SSF55785. SSF55785. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
TIGR00229. sensory_box. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
PS50113. PAC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P77302-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MITHNFNTLD LLTSPVWIVS PFEEQLIYAN SAAKLLMQDL TFSQLRTGPY
60 70 80 90 100
SVSSQKELPK YLSDLQNQHD IIEILTVQRK EEETALSCRL VLRKLTETEP
110 120 130 140 150
VIIFEGIEAP ATLGLKASRS ANYQRKKQGF YARFFLTNSA PMLLIDPSRD
160 170 180 190 200
GQIVDANLAA LNFYGYNHET MCQKHTWEIN MLGRRVMPIM HEISHLPGGH
210 220 230 240 250
KPLNFVHKLA DGSTRHVQTY AGPIEIYGDK LMLCIVHDIT EQKRLEEQLE
260 270 280 290 300
HAAHHDAMTG LLNRRQFYHI TEPGQMQHLA IAQDYSLLLI DTDRFKHIND
310 320 330 340 350
LYGHSKGDEV LCALARTLES CARKGDLVFR WGGEEFVLLL PRTPLDTALS
360 370 380 390 400
LAETIRVSVA KVSISGLPRF TVSIGVAHHE GNESIDELFK RVDDALYRAK
410
NDGRNRVLAA
Length:410
Mass (Da):46,452
Last modified:December 4, 2007 - v2
Checksum:i19FE87B41C540B62
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74423.2.
AP009048 Genomic DNA. Translation: BAA14945.2.
PIRiH64883.
RefSeqiNP_415857.2. NC_000913.3.
WP_000628058.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74423; AAC74423; b1341.
BAA14945; BAA14945; BAA14945.
GeneIDi945909.
KEGGiecj:JW5206.
eco:b1341.
PATRICi32117960. VBIEscCol129921_1400.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74423.2.
AP009048 Genomic DNA. Translation: BAA14945.2.
PIRiH64883.
RefSeqiNP_415857.2. NC_000913.3.
WP_000628058.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP77302.
SMRiP77302. Positions 256-407.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259650. 11 interactions.
DIPiDIP-28053N.
IntActiP77302. 6 interactions.
STRINGi511145.b1341.

Proteomic databases

PaxDbiP77302.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74423; AAC74423; b1341.
BAA14945; BAA14945; BAA14945.
GeneIDi945909.
KEGGiecj:JW5206.
eco:b1341.
PATRICi32117960. VBIEscCol129921_1400.

Organism-specific databases

EchoBASEiEB3138.
EcoGeneiEG13355. ydaM.

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
COG2199. LUCA.
COG2202. LUCA.
HOGENOMiHOG000120131.
InParanoidiP77302.
OMAiKLMLCII.
PhylomeDBiP77302.

Enzyme and pathway databases

UniPathwayiUPA00599.
BioCyciEcoCyc:G6673-MONOMER.
ECOL316407:JW5206-MONOMER.
MetaCyc:G6673-MONOMER.

Miscellaneous databases

PROiP77302.

Family and domain databases

CDDicd01949. GGDEF. 1 hit.
InterProiIPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR000014. PAS.
IPR000700. PAS-assoc_C.
IPR013656. PAS_4.
[Graphical view]
PfamiPF00990. GGDEF. 1 hit.
PF08448. PAS_4. 1 hit.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
SM00091. PAS. 2 hits.
[Graphical view]
SUPFAMiSSF55073. SSF55073. 1 hit.
SSF55785. SSF55785. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
TIGR00229. sensory_box. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
PS50113. PAC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYDAM_ECOLI
AccessioniPrimary (citable) accession number: P77302
Secondary accession number(s): P76846
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: December 4, 2007
Last modified: September 7, 2016
This is version 138 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

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. 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.