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Protein

Diguanylate cyclase DgcM

Gene

dgcM

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

Functioni

Part of a signaling cascade that regulates curli biosynthesis. The cascade is composed of two cyclic-di-GMP (c-di-GMP) control modules, in which c-di-GMP controlled by the DgcE/PdeH pair (module I) regulates the activity of the DgcM/PdeR pair (module II), which in turn regulates activity of the transcription factor MlrA and expression of the master biofilm regulator csgD (PubMed:23708798). DgcM stimulates activity of MlrA by direct interaction, leading to the transcription of csgD. It also catalyzes the synthesis of c-di-GMP via the condensation of 2 GTP molecules, which contributes to the c-di-GMP pool generated by module I in a positive feedback loop. Production of c-di-GMP contributes to but is not essential for MlrA activation (PubMed:17010156, PubMed:23708798).2 Publications

Catalytic activityi

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

Cofactori

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

Enzyme regulationi

Activity is inhibited by the phosphodiesterase PdeR. Inhibition is relieved by high cellular c-di-GMP levels.2 Publications

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.Curated
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)DescriptionActionsGraphical viewLength
Metal bindingi291MagnesiumBy similarity1
Sitei296Transition state stabilizerSequence analysis1
Binding sitei299SubstrateBy similarity1
Binding sitei304Substrate; via carbonyl oxygenBy similarity1
Binding sitei308SubstrateBy similarity1
Active sitei334Proton acceptorSequence analysis1
Metal bindingi334MagnesiumBy similarity1

GO - Molecular functioni

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

GO - Biological processi

  • positive regulation of DNA binding transcription factor activity Source: EcoCyc
  • positive regulation of single-species biofilm formation on inanimate substrate Source: EcoCyc

Keywordsi

Molecular functionTransferase
LigandGTP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:G6673-MONOMER
MetaCyc:G6673-MONOMER
UniPathwayiUPA00599

Names & Taxonomyi

Protein namesi
Recommended name:
Diguanylate cyclase DgcMCurated (EC:2.7.7.652 Publications)
Short name:
DGCCurated
Gene namesi
Name:dgcM1 Publication
Synonyms:ydaM
Ordered Locus Names:b1341, JW5206
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13355 ydaM

Subcellular locationi

GO - Cellular componenti

Pathology & Biotechi

Disruption phenotypei

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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi334 – 335EE → AA: No longer complements a dgcM disruption, loss of csgB induction. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002013131 – 410Diguanylate cyclase DgcMAdd BLAST410

Proteomic databases

PaxDbiP77302
PRIDEiP77302

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 DgcM and DosC are the major RpoS-dependent GGDEF-domain containing proteins in the cell. Expression is RpoS and H-NS dependent.2 Publications

Interactioni

Subunit structurei

Forms homodimers and homotetramers (PubMed:23708798). Interacts with PdeR and MlrA (PubMed:23708798).1 Publication

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4259650, 19 interactors
DIPiDIP-28053N
IntActiP77302, 7 interactors
MINTiP77302
STRINGi316385.ECDH10B_1462

Structurei

3D structure databases

ProteinModelPortaliP77302
SMRiP77302
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 70PAS 1Sequence analysisAdd BLAST68
Domaini129 – 198PAS 2Sequence analysisAdd BLAST70
Domaini199 – 251PACPROSITE-ProRule annotationAdd BLAST53
Domaini283 – 410GGDEFPROSITE-ProRule annotationAdd BLAST128

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiENOG4105BZU Bacteria
COG2199 LUCA
COG2202 LUCA
HOGENOMiHOG000120131
InParanoidiP77302
KOiK21088
OMAiKLMLCII
PhylomeDBiP77302

Family and domain databases

CDDicd01949 GGDEF, 1 hit
cd00130 PAS, 1 hit
InterProiView protein in InterPro
IPR000160 GGDEF_dom
IPR029787 Nucleotide_cyclase
IPR000014 PAS
IPR000700 PAS-assoc_C
IPR035965 PAS-like_dom_sf
IPR013656 PAS_4
PfamiView protein in Pfam
PF00990 GGDEF, 1 hit
PF08448 PAS_4, 1 hit
SMARTiView protein in SMART
SM00267 GGDEF, 1 hit
SM00091 PAS, 2 hits
SUPFAMiSSF55073 SSF55073, 1 hit
SSF55785 SSF55785, 1 hit
TIGRFAMsiTIGR00254 GGDEF, 1 hit
TIGR00229 sensory_box, 1 hit
PROSITEiView protein in PROSITE
PS50887 GGDEF, 1 hit
PS50113 PAC, 1 hit

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
PATRICifig|1411691.4.peg.936

Similar proteinsi

Entry informationi

Entry nameiDGCM_ECOLI
AccessioniPrimary (citable) accession number: P77302
Secondary accession number(s): P76846
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 27, 2002
Last sequence update: December 4, 2007
Last modified: May 23, 2018
This is version 151 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health