DGCZ_ECOLI
ID DGCZ_ECOLI Reviewed; 296 AA.
AC P31129; P76152; P77452;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 15-JUL-1998, sequence version 2.
DT 03-AUG-2022, entry version 156.
DE RecName: Full=Diguanylate cyclase DgcZ {ECO:0000303|PubMed:23769666};
DE Short=DGC {ECO:0000303|PubMed:18713317};
DE EC=2.7.7.65 {ECO:0000269|PubMed:19460094, ECO:0000269|PubMed:20582742, ECO:0000305|PubMed:18713317};
DE AltName: Full=Zinc-sensory diguanylate cyclase {ECO:0000303|PubMed:23769666};
GN Name=dgcZ {ECO:0000303|PubMed:23769666, ECO:0000303|PubMed:26148715};
GN Synonyms=ydeG, ydeH; OrderedLocusNames=b1535, JW1528;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8383113; DOI=10.1128/jb.175.5.1484-1492.1993;
RA Cohen S.P., Haechler H., Levy S.B.;
RT "Genetic and functional analysis of the multiple antibiotic resistance
RT (mar) locus in Escherichia coli.";
RL J. Bacteriol. 175:1484-1492(1993).
RN [2]
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 [3]
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 [4]
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 [5]
RP PROBABLE ENZYME ACTIVITY, MUTAGENESIS OF 206-GLY-GLY-207, DISRUPTION
RP PHENOTYPE, AND POST-TRANSCRIPTIONAL REGULATION BY CSRA.
RC STRAIN=K12;
RX PubMed=18713317; DOI=10.1111/j.1365-2958.2008.06411.x;
RA Jonas K., Edwards A.N., Simm R., Romeo T., Romling U., Melefors O.;
RT "The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly
RT regulating the expression of GGDEF proteins.";
RL Mol. Microbiol. 70:236-257(2008).
RN [6]
RP INDUCTION, AND RPOS-REPRESSION.
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 [7]
RP FUNCTION IN BIOFILM FORMATION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVITY REGULATION, SUBUNIT, MUTAGENESIS OF GLU-208, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / AB400;
RX PubMed=19460094; DOI=10.1111/j.1365-2958.2009.06739.x;
RA Boehm A., Steiner S., Zaehringer F., Casanova A., Hamburger F., Ritz D.,
RA Keck W., Ackermann M., Schirmer T., Jenal U.;
RT "Second messenger signalling governs Escherichia coli biofilm induction
RT upon ribosomal stress.";
RL Mol. Microbiol. 72:1500-1516(2009).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=20582742; DOI=10.1007/s12010-010-9017-x;
RA Zaehringer F., Massa C., Schirmer T.;
RT "Efficient enzymatic production of the bacterial second messenger c-di-GMP
RT by the diguanylate cyclase YdeH from E. coli.";
RL Appl. Biochem. Biotechnol. 163:71-79(2011).
RN [9]
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).
RN [10] {ECO:0007744|PDB:3T9O, ECO:0007744|PDB:3TVK, ECO:0007744|PDB:4H54}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 127-296 IN COMPLEXES WITH CYCLIC
RP DIGUANOSINE MONOPHOSPHATE; MAGNESIUM AND ZINC, FUNCTION, NOMENCLATURE,
RP COFACTOR, ACTIVITY REGULATION, SUBUNIT, DOMAIN, AND MUTAGENESIS OF CYS-52;
RP HIS-79 AND HIS-83.
RX PubMed=23769666; DOI=10.1016/j.str.2013.04.026;
RA Zahringer F., Lacanna E., Jenal U., Schirmer T., Boehm A.;
RT "Structure and signaling mechanism of a zinc-sensory diguanylate cyclase.";
RL Structure 21:1149-1157(2013).
CC -!- FUNCTION: Catalyzes the synthesis of cyclic-di-GMP (c-di-GMP) via the
CC condensation of 2 GTP molecules (PubMed:18713317, PubMed:19460094,
CC PubMed:20582742). May act as a zinc sensor that controls, via c-di-GMP,
CC post-translational events (PubMed:23769666). Overexpression leads to a
CC strong repression of swimming; swimming returnes to normal when
CC residues 206-207 are both mutated to Ala. Overexpression also leads to
CC a reduction in flagellar abundance and a 20-fold increase in c-di-GMP
CC levels in vivo. Required for aminoglycoside-mediated induction of
CC biofilm formation, it also plays a lesser role in biofilm production in
CC response to other classes of translation inhibitors. The c-di-GMP
CC produced by this enzyme up-regulates poly-GlcNAc production as well as
CC the biofilm synthesis protein PgaD, although c-di-GMP is probably not
CC the main inducing principle. C-di-GMP is a second messenger which
CC controls cell surface-associated traits in bacteria (PubMed:19460094).
CC {ECO:0000269|PubMed:19460094, ECO:0000269|PubMed:20582742,
CC ECO:0000269|PubMed:23769666, ECO:0000305|PubMed:18713317}.
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:19460094, ECO:0000269|PubMed:20582742,
CC ECO:0000305|PubMed:18713317};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:23769666};
CC Note=Binds 1 Mg(2+) ion per monomer. {ECO:0000269|PubMed:23769666};
CC -!- ACTIVITY REGULATION: Allosterically regulated by zinc, which seems to
CC regulate the activity of the catalytic GGDEF domains by impeding their
CC mobility and thus preventing productive encounter of the two GTP
CC substrates (PubMed:23769666). Subject to product inhibition by c-di-GMP
CC at a KI of 44 uM (PubMed:19460094). {ECO:0000269|PubMed:19460094,
CC ECO:0000269|PubMed:23769666}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=17 uM for GTP {ECO:0000269|PubMed:19460094};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:20582742};
CC -!- PATHWAY: Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.
CC {ECO:0000305}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:19460094,
CC ECO:0000269|PubMed:23769666}.
CC -!- INTERACTION:
CC P31129; P31129: dgcZ; NbExp=3; IntAct=EBI-1124405, EBI-1124405;
CC -!- INDUCTION: CsrA binds to the mRNA and reduces its levels. Expressed at
CC low levels at both 28 and 37 degrees Celsius. Repressed by RpoS.
CC {ECO:0000269|PubMed:18713317, ECO:0000269|PubMed:19332833}.
CC -!- DOMAIN: Contains an N-terminal CZB (chemoreceptor zinc binding) domain
CC and a C-terminal GGDEF domain. {ECO:0000269|PubMed:23769666}.
CC -!- DISRUPTION PHENOTYPE: A slight increase in motility. No visible effect
CC on curli production (PubMed:18713317). Decreased biofilm formation,
CC very little associated poly-GlcNAc production, and a complete loss of
CC aminoglycoside-mediated induction of biofilm formation
CC (PubMed:19460094). {ECO:0000269|PubMed:18713317,
CC ECO:0000269|PubMed:19460094}.
CC -!- SEQUENCE CAUTION:
CC Sequence=M96235; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; M96235; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U00096; AAC74608.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA18882.2; -; Genomic_DNA.
DR PIR; B64908; B64908.
DR RefSeq; NP_416052.1; NC_000913.3.
DR RefSeq; WP_000592814.1; NZ_SSZK01000001.1.
DR PDB; 3T9O; X-ray; 2.20 A; A/B=2-126.
DR PDB; 3TVK; X-ray; 1.80 A; A=127-296.
DR PDB; 4H54; X-ray; 3.90 A; A/B=2-296.
DR PDBsum; 3T9O; -.
DR PDBsum; 3TVK; -.
DR PDBsum; 4H54; -.
DR AlphaFoldDB; P31129; -.
DR SMR; P31129; -.
DR BioGRID; 4259114; 10.
DR DIP; DIP-11677N; -.
DR IntAct; P31129; 6.
DR STRING; 511145.b1535; -.
DR PaxDb; P31129; -.
DR PRIDE; P31129; -.
DR EnsemblBacteria; AAC74608; AAC74608; b1535.
DR EnsemblBacteria; BAA18882; BAA18882; BAA18882.
DR GeneID; 946075; -.
DR KEGG; ecj:JW1528; -.
DR KEGG; eco:b1535; -.
DR PATRIC; fig|511145.12.peg.1605; -.
DR EchoBASE; EB1596; -.
DR eggNOG; COG3706; Bacteria.
DR HOGENOM; CLU_000445_11_5_6; -.
DR InParanoid; P31129; -.
DR OMA; NIRSNMD; -.
DR PhylomeDB; P31129; -.
DR BioCyc; EcoCyc:EG11643-MON; -.
DR BioCyc; MetaCyc:EG11643-MON; -.
DR BRENDA; 2.7.7.65; 2026.
DR SABIO-RK; P31129; -.
DR UniPathway; UPA00599; -.
DR PRO; PR:P31129; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0060187; C:cell pole; IDA:EcoCyc.
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; IPI:IntAct.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0043709; P:cell adhesion involved in single-species biofilm formation; IMP:EcoCyc.
DR GO; GO:0008152; P:metabolic process; IEA:UniProtKB-KW.
DR GO; GO:1902209; P:negative regulation of bacterial-type flagellum assembly; IMP:EcoCyc.
DR GO; GO:1902201; P:negative regulation of bacterial-type flagellum-dependent cell motility; IBA:GO_Central.
DR GO; GO:1900233; P:positive regulation of single-species biofilm formation on inanimate substrate; IMP:EcoCyc.
DR CDD; cd01949; GGDEF; 1.
DR Gene3D; 3.30.70.270; -; 1.
DR InterPro; IPR000160; GGDEF_dom.
DR InterPro; IPR029787; Nucleotide_cyclase.
DR InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR Pfam; PF00990; GGDEF; 1.
DR SMART; SM00267; GGDEF; 1.
DR SUPFAM; SSF55073; SSF55073; 1.
DR TIGRFAMs; TIGR00254; GGDEF; 1.
DR PROSITE; PS50887; GGDEF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Allosteric enzyme; GTP-binding; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..296
FT /note="Diguanylate cyclase DgcZ"
FT /id="PRO_0000168946"
FT DOMAIN 157..289
FT /note="GGDEF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00095"
FT ACT_SITE 208
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT BINDING 22
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:23769666,
FT ECO:0007744|PDB:3T9O, ECO:0007744|PDB:4H54"
FT BINDING 52
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:23769666,
FT ECO:0007744|PDB:3T9O"
FT BINDING 79
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:23769666,
FT ECO:0007744|PDB:3T9O, ECO:0007744|PDB:4H54"
FT BINDING 83
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:23769666,
FT ECO:0007744|PDB:3T9O, ECO:0007744|PDB:4H54"
FT BINDING 165
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23769666,
FT ECO:0007744|PDB:4H54"
FT BINDING 166
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23769666,
FT ECO:0007744|PDB:4H54"
FT BINDING 173
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23769666"
FT BINDING 178
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23769666"
FT BINDING 182
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23769666"
FT BINDING 195..200
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23769666"
FT BINDING 208
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:23769666,
FT ECO:0007744|PDB:4H54"
FT BINDING 215
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23769666"
FT BINDING 224
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23769666"
FT BINDING 228
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23769666"
FT SITE 170
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000255"
FT MUTAGEN 52
FT /note="C->A: Decreases zinc affinity by one order of
FT magnitude."
FT /evidence="ECO:0000269|PubMed:23769666"
FT MUTAGEN 79
FT /note="H->L: Displays constitutively high biofilm and PgaD
FT levels; when associated with L-83."
FT /evidence="ECO:0000269|PubMed:23769666"
FT MUTAGEN 83
FT /note="H->L: Displays constitutively high biofilm and PgaD
FT levels; when associated with L-79."
FT /evidence="ECO:0000269|PubMed:23769666"
FT MUTAGEN 206..207
FT /note="GG->AA: Cells overexpressing this mutant are no
FT longer swimming suppressed."
FT /evidence="ECO:0000269|PubMed:18713317"
FT MUTAGEN 208
FT /note="E->Q: Significantly decreased biofilm formation."
FT /evidence="ECO:0000269|PubMed:19460094"
FT HELIX 6..35
FT /evidence="ECO:0007829|PDB:3T9O"
FT HELIX 41..44
FT /evidence="ECO:0007829|PDB:3T9O"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:3T9O"
FT HELIX 53..59
FT /evidence="ECO:0007829|PDB:3T9O"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:3T9O"
FT HELIX 69..94
FT /evidence="ECO:0007829|PDB:3T9O"
FT HELIX 100..125
FT /evidence="ECO:0007829|PDB:3T9O"
FT TURN 133..135
FT /evidence="ECO:0007829|PDB:3TVK"
FT HELIX 140..152
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 157..166
FT /evidence="ECO:0007829|PDB:3TVK"
FT HELIX 169..176
FT /evidence="ECO:0007829|PDB:3TVK"
FT HELIX 178..194
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 202..204
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 206..218
FT /evidence="ECO:0007829|PDB:3TVK"
FT HELIX 219..235
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 249..256
FT /evidence="ECO:0007829|PDB:3TVK"
FT HELIX 262..278
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 281..287
FT /evidence="ECO:0007829|PDB:3TVK"
FT STRAND 293..295
FT /evidence="ECO:0007829|PDB:3TVK"
SQ SEQUENCE 296 AA; 33863 MW; 7B6884E6B8A6D8D8 CRC64;
MIKKTTEIDA ILLNLNKAID AHYQWLVSMF HSVVARDASK PEITDNHSYG LCQFGRWIDH
LGPLDNDELP YVRLMDSAHQ HMHNCGRELM LAIVENHWQD AHFDAFQEGL LSFTAALTDY
KIYLLTIRSN MDVLTGLPGR RVLDESFDHQ LRNAEPLNLY LMLLDIDRFK LVNDTYGHLI
GDVVLRTLAT YLASWTRDYE TVYRYGGEEF IIIVKAANDE EACRAGVRIC QLVDNHAITH
SEGHINITVT AGVSRAFPEE PLDVVIGRAD RAMYEGKQTG RNRCMFIDEQ NVINRV
