DGCM_ECOLI
ID DGCM_ECOLI Reviewed; 410 AA.
AC P77302; P76846;
DT 27-MAR-2002, integrated into UniProtKB/Swiss-Prot.
DT 04-DEC-2007, sequence version 2.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=Diguanylate cyclase DgcM {ECO:0000305};
DE Short=DGC {ECO:0000305};
DE EC=2.7.7.65 {ECO:0000269|PubMed:17010156, ECO:0000269|PubMed:23708798};
GN Name=dgcM {ECO:0000303|PubMed:26148715}; Synonyms=ydaM;
GN OrderedLocusNames=b1341, JW5206;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP FUNCTION IN FIMBRIAE EXPRESSION, CATALYTIC ACTIVITY, ACTIVITY REGULATION,
RP MUTAGENESIS OF 334-GLU-GLU-335, INDUCTION, RPOS- AND H-NS-DEPENDENCE, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC4100;
RX PubMed=17010156; DOI=10.1111/j.1365-2958.2006.05440.x;
RA Weber H., Pesavento C., Possling A., Tischendorf G., Hengge R.;
RT "Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia
RT coli.";
RL Mol. Microbiol. 62:1014-1034(2006).
RN [5]
RP INDUCTION, RPOS-DEPENDENCE, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=19332833; DOI=10.1099/mic.0.024257-0;
RA Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N.,
RA Hengge R.;
RT "Gene expression patterns and differential input into curli fimbriae
RT regulation of all GGDEF/EAL domain proteins in Escherichia coli.";
RL Microbiology 155:1318-1331(2009).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND INTERACTION WITH
RP PDER AND MLRA.
RX PubMed=23708798; DOI=10.1038/emboj.2013.120;
RA Lindenberg S., Klauck G., Pesavento C., Klauck E., Hengge R.;
RT "The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP
RT signalling cascade in E. coli biofilm control.";
RL EMBO J. 32:2001-2014(2013).
RN [7]
RP NOMENCLATURE.
RX PubMed=26148715; DOI=10.1128/jb.00424-15;
RA Hengge R., Galperin M.Y., Ghigo J.M., Gomelsky M., Green J., Hughes K.T.,
RA Jenal U., Landini P.;
RT "Systematic nomenclature for GGDEF and EAL domain-containing cyclic di-GMP
RT turnover proteins of Escherichia coli.";
RL J. Bacteriol. 198:7-11(2015).
CC -!- FUNCTION: Part of a signaling cascade that regulates curli
CC biosynthesis. The cascade is composed of two cyclic-di-GMP (c-di-GMP)
CC control modules, in which c-di-GMP controlled by the DgcE/PdeH pair
CC (module I) regulates the activity of the DgcM/PdeR pair (module II),
CC which in turn regulates activity of the transcription factor MlrA and
CC expression of the master biofilm regulator csgD (PubMed:23708798). DgcM
CC stimulates activity of MlrA by direct interaction, leading to the
CC transcription of csgD. It also catalyzes the synthesis of c-di-GMP via
CC the condensation of 2 GTP molecules, which contributes to the c-di-GMP
CC pool generated by module I in a positive feedback loop. Production of
CC c-di-GMP contributes to but is not essential for MlrA activation
CC (PubMed:17010156, PubMed:23708798). {ECO:0000269|PubMed:17010156,
CC ECO:0000269|PubMed:23708798}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate;
CC Xref=Rhea:RHEA:24898, ChEBI:CHEBI:33019, ChEBI:CHEBI:37565,
CC ChEBI:CHEBI:58805; EC=2.7.7.65;
CC Evidence={ECO:0000269|PubMed:17010156, ECO:0000269|PubMed:23708798};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P31129};
CC Note=Binds 1 Mg(2+) ion per monomer. {ECO:0000250|UniProtKB:P31129};
CC -!- ACTIVITY REGULATION: Activity is inhibited by the phosphodiesterase
CC PdeR. Inhibition is relieved by high cellular c-di-GMP levels.
CC {ECO:0000269|PubMed:17010156, ECO:0000269|PubMed:23708798}.
CC -!- PATHWAY: Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.
CC {ECO:0000305}.
CC -!- SUBUNIT: Forms homodimers and homotetramers (PubMed:23708798).
CC Interacts with PdeR and MlrA (PubMed:23708798).
CC {ECO:0000269|PubMed:23708798}.
CC -!- INTERACTION:
CC P77302; P77302: dgcM; NbExp=3; IntAct=EBI-544662, EBI-544662;
CC P77302; P33358: mlrA; NbExp=2; IntAct=EBI-544662, EBI-1127668;
CC P77302; P77334: pdeR; NbExp=5; IntAct=EBI-544662, EBI-548149;
CC -!- INDUCTION: Expressed during transition into stationary phase,
CC expression is higher at 28 than 37 degrees Celsius, more highly
CC expressed on plates than in liquid medium. In rich medium DgcM and DosC
CC are the major RpoS-dependent GGDEF-domain containing proteins in the
CC cell. Expression is RpoS and H-NS dependent.
CC {ECO:0000269|PubMed:17010156, ECO:0000269|PubMed:19332833}.
CC -!- DISRUPTION PHENOTYPE: Loss of curli fimbriae, decreased biofilm
CC formation, decreased expression of DgcC, a probable diguanylate cyclase
CC and of the curli regulator CsgD. {ECO:0000269|PubMed:17010156,
CC ECO:0000269|PubMed:19332833}.
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DR EMBL; U00096; AAC74423.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA14945.2; -; Genomic_DNA.
DR PIR; H64883; H64883.
DR RefSeq; NP_415857.2; NC_000913.3.
DR RefSeq; WP_000628058.1; NZ_SSZK01000012.1.
DR AlphaFoldDB; P77302; -.
DR SMR; P77302; -.
DR BioGRID; 4259650; 19.
DR DIP; DIP-28053N; -.
DR IntAct; P77302; 7.
DR MINT; P77302; -.
DR STRING; 511145.b1341; -.
DR jPOST; P77302; -.
DR PaxDb; P77302; -.
DR PRIDE; P77302; -.
DR EnsemblBacteria; AAC74423; AAC74423; b1341.
DR EnsemblBacteria; BAA14945; BAA14945; BAA14945.
DR GeneID; 945909; -.
DR KEGG; ecj:JW5206; -.
DR KEGG; eco:b1341; -.
DR PATRIC; fig|1411691.4.peg.936; -.
DR EchoBASE; EB3138; -.
DR eggNOG; COG3706; Bacteria.
DR HOGENOM; CLU_000445_11_4_6; -.
DR InParanoid; P77302; -.
DR OMA; HTWEINT; -.
DR PhylomeDB; P77302; -.
DR BioCyc; EcoCyc:G6673-MON; -.
DR BioCyc; MetaCyc:G6673-MON; -.
DR UniPathway; UPA00599; -.
DR PRO; PR:P77302; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0052621; F:diguanylate cyclase activity; IDA:EcoCyc.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043709; P:cell adhesion involved in single-species biofilm formation; IBA:GO_Central.
DR GO; GO:1902201; P:negative regulation of bacterial-type flagellum-dependent cell motility; IBA:GO_Central.
DR GO; GO:0051091; P:positive regulation of DNA-binding transcription factor activity; IMP:EcoCyc.
DR GO; GO:1900233; P:positive regulation of single-species biofilm formation on inanimate substrate; IMP:EcoCyc.
DR CDD; cd01949; GGDEF; 1.
DR CDD; cd00130; PAS; 1.
DR Gene3D; 3.30.70.270; -; 1.
DR InterPro; IPR000160; GGDEF_dom.
DR InterPro; IPR029787; Nucleotide_cyclase.
DR InterPro; IPR000014; PAS.
DR InterPro; IPR000700; PAS-assoc_C.
DR InterPro; IPR035965; PAS-like_dom_sf.
DR InterPro; IPR013656; PAS_4.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR Pfam; PF00990; GGDEF; 1.
DR Pfam; PF08448; PAS_4; 1.
DR SMART; SM00267; GGDEF; 1.
DR SMART; SM00091; PAS; 2.
DR SUPFAM; SSF55073; SSF55073; 1.
DR SUPFAM; SSF55785; SSF55785; 1.
DR TIGRFAMs; TIGR00254; GGDEF; 1.
DR TIGRFAMs; TIGR00229; sensory_box; 1.
DR PROSITE; PS50887; GGDEF; 1.
DR PROSITE; PS50113; PAC; 1.
PE 1: Evidence at protein level;
KW GTP-binding; Magnesium; Metal-binding; Nucleotide-binding;
KW Reference proteome; Repeat; Transferase.
FT CHAIN 1..410
FT /note="Diguanylate cyclase DgcM"
FT /id="PRO_0000201313"
FT DOMAIN 3..70
FT /note="PAS 1"
FT /evidence="ECO:0000255"
FT DOMAIN 129..198
FT /note="PAS 2"
FT /evidence="ECO:0000255"
FT DOMAIN 199..251
FT /note="PAC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00141"
FT DOMAIN 283..410
FT /note="GGDEF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00095"
FT ACT_SITE 334
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT BINDING 291
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P31129"
FT BINDING 299
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P31129"
FT BINDING 304
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P31129"
FT BINDING 308
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P31129"
FT BINDING 334
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P31129"
FT SITE 296
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255"
FT MUTAGEN 334..335
FT /note="EE->AA: No longer complements a dgcM disruption,
FT loss of csgB induction."
FT /evidence="ECO:0000269|PubMed:17010156"
SQ SEQUENCE 410 AA; 46452 MW; 19FE87B41C540B62 CRC64;
MITHNFNTLD LLTSPVWIVS PFEEQLIYAN SAAKLLMQDL TFSQLRTGPY SVSSQKELPK
YLSDLQNQHD IIEILTVQRK EEETALSCRL VLRKLTETEP VIIFEGIEAP ATLGLKASRS
ANYQRKKQGF YARFFLTNSA PMLLIDPSRD GQIVDANLAA LNFYGYNHET MCQKHTWEIN
MLGRRVMPIM HEISHLPGGH KPLNFVHKLA DGSTRHVQTY AGPIEIYGDK LMLCIVHDIT
EQKRLEEQLE HAAHHDAMTG LLNRRQFYHI TEPGQMQHLA IAQDYSLLLI DTDRFKHIND
LYGHSKGDEV LCALARTLES CARKGDLVFR WGGEEFVLLL PRTPLDTALS LAETIRVSVA
KVSISGLPRF TVSIGVAHHE GNESIDELFK RVDDALYRAK NDGRNRVLAA
