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Response regulator PleD (Stalked cell differentiation-controlling protein) [Includes: Diguanylate cyclase (DGC) (EC 2.7.7.65) (Diguanylate kinase)]

 PLED_CAUVN              Reviewed;         454 AA.
B8GZM2;
10-AUG-2010, integrated into UniProtKB/Swiss-Prot.
03-MAR-2009, sequence version 1.
05-DEC-2018, entry version 69.
RecName: Full=Response regulator PleD;
AltName: Full=Stalked cell differentiation-controlling protein;
Includes:
RecName: Full=Diguanylate cyclase;
Short=DGC;
EC=2.7.7.65 {ECO:0000269|PubMed:15075296};
AltName: Full=Diguanylate kinase;
Name=pleD; OrderedLocusNames=CCNA_02546;
Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter
crescentus).
Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales;
Caulobacteraceae; Caulobacter.
NCBI_TaxID=565050;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=NA1000 / CB15N;
PubMed=20472802; DOI=10.1128/JB.00255-10;
Marks M.E., Castro-Rojas C.M., Teiling C., Du L., Kapatral V.,
Walunas T.L., Crosson S.;
"The genetic basis of laboratory adaptation in Caulobacter
crescentus.";
J. Bacteriol. 192:3678-3688(2010).
[2]
ROLE IN POLAR DEVELOPMENT, AND PHOSPHORYLATION AT ASP-53.
PubMed=12622822; DOI=10.1046/j.1365-2958.2003.03401.x;
Aldridge P., Paul R., Goymer P., Rainey P., Jenal U.;
"Role of the GGDEF regulator PleD in polar development of Caulobacter
crescentus.";
Mol. Microbiol. 47:1695-1708(2003).
[3]
FUNCTION AS A NUCLEOTIDE CYCLASE, CELL POLE LOCALIZATION, AND
PHOSPHORYLATION AT ASP-53.
PubMed=15075296; DOI=10.1101/gad.289504;
Paul R., Weiser S., Amiot N.C., Chan C., Schirmer T., Giese B.,
Jenal U.;
"Cell cycle-dependent dynamic localization of a bacterial response
regulator with a novel di-guanylate cyclase output domain.";
Genes Dev. 18:715-727(2004).
[4] {ECO:0000244|PDB:1W25}
X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH C-DI-GMP,
ALLOSTERIC REGULATION, AND SUBUNIT.
PubMed=15569936; DOI=10.1073/pnas.0406134101;
Chan C., Paul R., Samoray D., Amiot N.C., Giese B., Jenal U.,
Schirmer T.;
"Structural basis of activity and allosteric control of diguanylate
cyclase.";
Proc. Natl. Acad. Sci. U.S.A. 101:17084-17089(2004).
[5] {ECO:0000244|PDB:2V0N}
X-RAY CRYSTALLOGRAPHY (2.71 ANGSTROMS) OF 2-454 OF DIMER WITH C-DI-GMP
IN THE ACTIVATED FORM, AND COFACTOR.
PubMed=17697997; DOI=10.1016/j.str.2007.06.016;
Wassmann P., Chan C., Paul R., Beck A., Heerklotz H., Jenal U.,
Schirmer T.;
"Structure of BeF(3-)-modified response regulator PleD: implications
for diguanylate cyclase activation, catalysis, and feedback
inhibition.";
Structure 15:915-927(2007).
[6] {ECO:0000244|PDB:2WB4}
X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS).
Wassmann P., Massa C., Zaehringer F., Schirmer T.;
"Crystal structure of activated Pled, identification of dimerization
and catalysis relevant regulatory mechanisms.";
Submitted (FEB-2009) to the PDB data bank.
-!- FUNCTION: Response regulator that is part of a signal transduction
pathway controlling cell differentiation in the swarmer-to-stalked
cell transition. {ECO:0000269|PubMed:12622822}.
-!- FUNCTION: Catalyzes the condensation of two GTP molecules to the
cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary
messenger. {ECO:0000269|PubMed:15075296}.
-!- CATALYTIC ACTIVITY:
Reaction=2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate;
Xref=Rhea:RHEA:24898, ChEBI:CHEBI:33019, ChEBI:CHEBI:37565,
ChEBI:CHEBI:58805; EC=2.7.7.65;
Evidence={ECO:0000269|PubMed:15075296};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:17697997};
Note=Binds 2 Mg(2+) per monomer. {ECO:0000269|PubMed:17697997};
-!- ACTIVITY REGULATION: Allosterically inhibited by dimers of the
product c-di-GMP. {ECO:0000269|PubMed:15569936}.
-!- PATHWAY: Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.
-!- SUBUNIT: Homodimer. Inactive monomer in solution, dimerization
seems to be required for activity. Dimerization in vitro is
enhanced by BeF(3-) and by 1 mM Mn(2+) or 10 mM Mg(2+).
{ECO:0000269|PubMed:15569936}.
-!- SUBCELLULAR LOCATION: Cytoplasm. Note=Phosphorylated PleD
localizes to the differentiating pole.
{ECO:0000269|PubMed:15075296}.
-!- DOMAIN: Activated by phosphorylation at the first response
regulatory domain, which induces dimerization mediated by the two
response regulatory domains and allows the two substrate-binding
sites to approach each other and the condensation reaction to
occur (Probable). The diguanylate cyclase activity is harbored by
the GGDEF domain. {ECO:0000305}.
-!- PTM: Phosphorylated by PleC and DivJ. Phosphorylation stimulates
cyclase activity. {ECO:0000269|PubMed:12622822,
ECO:0000269|PubMed:15075296}.
-----------------------------------------------------------------------
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EMBL; CP001340; ACL96011.1; -; Genomic_DNA.
RefSeq; WP_010920320.1; NC_011916.1.
RefSeq; YP_002517919.1; NC_011916.1.
PDB; 1W25; X-ray; 2.70 A; A/B=2-454.
PDB; 2V0N; X-ray; 2.71 A; A/B=2-454.
PDB; 2WB4; X-ray; 2.80 A; A/B=1-454.
PDBsum; 1W25; -.
PDBsum; 2V0N; -.
PDBsum; 2WB4; -.
ProteinModelPortal; B8GZM2; -.
SMR; B8GZM2; -.
PRIDE; B8GZM2; -.
EnsemblBacteria; ACL96011; ACL96011; CCNA_02546.
GeneID; 7333643; -.
KEGG; ccs:CCNA_02546; -.
PATRIC; fig|565050.3.peg.2497; -.
HOGENOM; HOG000167204; -.
KO; K02488; -.
OMA; NDYFVYP; -.
OrthoDB; POG091H049G; -.
UniPathway; UPA00599; -.
EvolutionaryTrace; B8GZM2; -.
Proteomes; UP000001364; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0052621; F:diguanylate cyclase activity; IEA:UniProtKB-EC.
GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
GO; GO:0000160; P:phosphorelay signal transduction system; IEA:UniProtKB-KW.
CDD; cd01949; GGDEF; 1.
CDD; cd00156; REC; 1.
InterPro; IPR011006; CheY-like_superfamily.
InterPro; IPR000160; GGDEF_dom.
InterPro; IPR029787; Nucleotide_cyclase.
InterPro; IPR001789; Sig_transdc_resp-reg_receiver.
Pfam; PF00990; GGDEF; 1.
Pfam; PF00072; Response_reg; 2.
SMART; SM00267; GGDEF; 1.
SMART; SM00448; REC; 2.
SUPFAM; SSF52172; SSF52172; 2.
SUPFAM; SSF55073; SSF55073; 1.
TIGRFAMs; TIGR00254; GGDEF; 1.
PROSITE; PS50887; GGDEF; 1.
PROSITE; PS50110; RESPONSE_REGULATORY; 2.
1: Evidence at protein level;
3D-structure; Cell cycle; Complete proteome; Cytoplasm;
Differentiation; GTP-binding; Magnesium; Metal-binding;
Nucleotide-binding; Phosphoprotein; Reference proteome; Repeat;
Transducer; Transferase; Two-component regulatory system.
CHAIN 1 454 Response regulator PleD.
/FTId=PRO_0000396955.
DOMAIN 4 120 Response regulatory 1.
{ECO:0000255|PROSITE-ProRule:PRU00169}.
DOMAIN 155 269 Response regulatory 2.
{ECO:0000255|PROSITE-ProRule:PRU00169}.
DOMAIN 319 454 GGDEF. {ECO:0000255|PROSITE-
ProRule:PRU00095}.
ACT_SITE 370 370 Proton acceptor. {ECO:0000255}.
METAL 9 9 Magnesium 1.
{ECO:0000269|PubMed:15569936}.
METAL 10 10 Magnesium 1.
{ECO:0000269|PubMed:15569936,
ECO:0000269|PubMed:17697997,
ECO:0000269|Ref.6}.
METAL 53 53 Magnesium 1.
{ECO:0000269|PubMed:15569936,
ECO:0000269|PubMed:17697997,
ECO:0000269|Ref.6}.
METAL 55 55 Magnesium 1; via carbonyl oxygen.
{ECO:0000269|PubMed:15569936,
ECO:0000269|PubMed:17697997,
ECO:0000269|Ref.6}.
METAL 327 327 Magnesium 2.
{ECO:0000269|PubMed:17697997}.
METAL 328 328 Magnesium 2; via carbonyl oxygen.
{ECO:0000269|PubMed:17697997}.
METAL 370 370 Magnesium 2.
{ECO:0000269|PubMed:17697997}.
BINDING 335 335 Substrate. {ECO:0000305|PubMed:15569936,
ECO:0000305|Ref.6}.
BINDING 344 344 Substrate. {ECO:0000305|PubMed:15569936,
ECO:0000305|Ref.6}.
SITE 178 178 Allosteric product binding, non-activate
state.
SITE 313 313 Allosteric product binding, active state.
SITE 332 332 Transition state stabilizer.
{ECO:0000255}.
SITE 359 359 Allosteric product phosphate group
binding, activate and inactive state.
SITE 362 362 Allosteric product binding, activate and
inactive state.
SITE 390 390 Allosteric product binding, activate and
inactive state.
MOD_RES 53 53 4-aspartylphosphate.
{ECO:0000255|PROSITE-ProRule:PRU00169,
ECO:0000269|PubMed:12622822,
ECO:0000269|PubMed:15075296}.
STRAND 4 8 {ECO:0000244|PDB:1W25}.
HELIX 14 24 {ECO:0000244|PDB:1W25}.
STRAND 28 34 {ECO:0000244|PDB:1W25}.
HELIX 35 45 {ECO:0000244|PDB:1W25}.
STRAND 48 54 {ECO:0000244|PDB:1W25}.
STRAND 57 59 {ECO:0000244|PDB:1W25}.
HELIX 61 70 {ECO:0000244|PDB:1W25}.
TURN 72 76 {ECO:0000244|PDB:1W25}.
STRAND 79 83 {ECO:0000244|PDB:1W25}.
HELIX 88 97 {ECO:0000244|PDB:1W25}.
STRAND 101 106 {ECO:0000244|PDB:1W25}.
HELIX 109 133 {ECO:0000244|PDB:1W25}.
TURN 134 137 {ECO:0000244|PDB:1W25}.
TURN 140 143 {ECO:0000244|PDB:1W25}.
HELIX 146 148 {ECO:0000244|PDB:2WB4}.
STRAND 151 153 {ECO:0000244|PDB:2WB4}.
STRAND 155 159 {ECO:0000244|PDB:1W25}.
HELIX 163 173 {ECO:0000244|PDB:1W25}.
TURN 174 176 {ECO:0000244|PDB:1W25}.
STRAND 177 182 {ECO:0000244|PDB:1W25}.
HELIX 185 193 {ECO:0000244|PDB:1W25}.
STRAND 197 202 {ECO:0000244|PDB:1W25}.
STRAND 206 208 {ECO:0000244|PDB:1W25}.
HELIX 210 218 {ECO:0000244|PDB:1W25}.
HELIX 221 223 {ECO:0000244|PDB:1W25}.
STRAND 228 232 {ECO:0000244|PDB:1W25}.
HELIX 237 245 {ECO:0000244|PDB:1W25}.
STRAND 250 255 {ECO:0000244|PDB:1W25}.
HELIX 258 279 {ECO:0000244|PDB:1W25}.
STRAND 280 283 {ECO:0000244|PDB:1W25}.
HELIX 284 286 {ECO:0000244|PDB:2V0N}.
STRAND 289 291 {ECO:0000244|PDB:2WB4}.
TURN 293 295 {ECO:0000244|PDB:1W25}.
HELIX 300 315 {ECO:0000244|PDB:1W25}.
STRAND 322 328 {ECO:0000244|PDB:1W25}.
HELIX 331 337 {ECO:0000244|PDB:1W25}.
HELIX 340 356 {ECO:0000244|PDB:1W25}.
STRAND 362 366 {ECO:0000244|PDB:1W25}.
STRAND 368 376 {ECO:0000244|PDB:1W25}.
HELIX 381 396 {ECO:0000244|PDB:1W25}.
STRAND 400 402 {ECO:0000244|PDB:2V0N}.
HELIX 403 405 {ECO:0000244|PDB:1W25}.
STRAND 407 409 {ECO:0000244|PDB:2V0N}.
STRAND 413 419 {ECO:0000244|PDB:1W25}.
HELIX 427 443 {ECO:0000244|PDB:1W25}.
STRAND 449 451 {ECO:0000244|PDB:1W25}.
SEQUENCE 454 AA; 49624 MW; D44909D42B581516 CRC64;
MSARILVVDD IEANVRLLEA KLTAEYYEVS TAMDGPTALA MAARDLPDII LLDVMMPGMD
GFTVCRKLKD DPTTRHIPVV LITALDGRGD RIQGLESGAS DFLTKPIDDV MLFARVRSLT
RFKLVIDELR QREASGRRMG VIAGAAARLD GLGGRVLIVD DNERQAQRVA AELGVEHRPV
IESDPEKAKI SAGGPVDLVI VNAAAKNFDG LRFTAALRSE ERTRQLPVLA MVDPDDRGRM
VKALEIGVND ILSRPIDPQE LSARVKTQIQ RKRYTDYLRN NLDHSLELAV TDQLTGLHNR
RYMTGQLDSL VKRATLGGDP VSALLIDIDF FKKINDTFGH DIGDEVLREF ALRLASNVRA
IDLPCRYGGE EFVVIMPDTA LADALRIAER IRMHVSGSPF TVAHGREMLN VTISIGVSAT
AGEGDTPEAL LKRADEGVYQ AKASGRNAVV GKAA


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