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Cyclic-di-AMP phosphodiesterase GdpP (c-di-AMP phosphodiesterase YybT) (EC 3.1.4.-) (Cyclic-di-AMP hydrolase GdpP) (Cyclic-di-AMP phosphodiesterase YybT)

 GDPP_BACSU              Reviewed;         659 AA.
P37484;
01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
01-OCT-1994, sequence version 1.
12-SEP-2018, entry version 101.
RecName: Full=Cyclic-di-AMP phosphodiesterase GdpP {ECO:0000303|PubMed:22211522};
Short=c-di-AMP phosphodiesterase YybT {ECO:0000303|PubMed:19901023};
EC=3.1.4.- {ECO:0000269|PubMed:19901023};
AltName: Full=Cyclic-di-AMP hydrolase GdpP {ECO:0000303|PubMed:22956758};
AltName: Full=Cyclic-di-AMP phosphodiesterase YybT;
Name=gdpP {ECO:0000303|PubMed:22211522}; Synonyms=yybT;
OrderedLocusNames=BSU40510;
Bacillus subtilis (strain 168).
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
NCBI_TaxID=224308;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=168;
PubMed=7584024; DOI=10.1093/dnares/1.1.1;
Ogasawara N., Nakai S., Yoshikawa H.;
"Systematic sequencing of the 180 kilobase region of the Bacillus
subtilis chromosome containing the replication origin.";
DNA Res. 1:1-14(1994).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=168;
PubMed=9384377; DOI=10.1038/36786;
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G.,
Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S.,
Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S.,
Brouillet S., Bruschi C.V., Caldwell B., Capuano V., Carter N.M.,
Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A.,
Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T.,
Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D.,
Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N.,
Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G.,
Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A.,
Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M.,
Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M.,
Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S.,
Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G.,
Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B.,
Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R.,
Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P.,
Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H.,
Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P.,
Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F.,
Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H.,
Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
Yoshikawa H., Danchin A.;
"The complete genome sequence of the Gram-positive bacterium Bacillus
subtilis.";
Nature 390:249-256(1997).
[3]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
BIOPHYSICOCHEMICAL PROPERTIES, DOMAIN, DISRUPTION PHENOTYPE, PROBABLE
TOPOLOGY, AND MUTAGENESIS OF ASP-183; GLU-225; ARG-291 AND ASP-420.
STRAIN=168;
PubMed=19901023; DOI=10.1074/jbc.M109.040238;
Rao F., See R.Y., Zhang D., Toh D.C., Ji Q., Liang Z.X.;
"YybT is a signaling protein that contains a cyclic dinucleotide
phosphodiesterase domain and a GGDEF domain with ATPase activity.";
J. Biol. Chem. 285:473-482(2010).
[4]
FUNCTION, ACTIVITY REGULATION, COFACTOR, AND DOMAIN.
STRAIN=168;
PubMed=21257773; DOI=10.1128/JB.01364-10;
Rao F., Ji Q., Soehano I., Liang Z.X.;
"Unusual heme-binding PAS domain from YybT family proteins.";
J. Bacteriol. 193:1543-1551(2011).
[5]
SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
STRAIN=168 / PY79;
PubMed=21566650; DOI=10.1038/embor.2011.77;
Oppenheimer-Shaanan Y., Wexselblatt E., Katzhendler J., Yavin E.,
Ben-Yehuda S.;
"c-di-AMP reports DNA integrity during sporulation in Bacillus
subtilis.";
EMBO Rep. 12:594-601(2011).
[6]
FUNCTION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF ASP-420.
STRAIN=168;
PubMed=22211522; DOI=10.1111/j.1365-2958.2011.07953.x;
Luo Y., Helmann J.D.;
"Analysis of the role of Bacillus subtilis sigma(M) in beta-lactam
resistance reveals an essential role for c-di-AMP in peptidoglycan
homeostasis.";
Mol. Microbiol. 83:623-639(2012).
[7]
INDUCTION.
PubMed=22956758; DOI=10.1099/mic.0.062174-0;
Luo Y., Helmann J.D.;
"A sigmaD-dependent antisense transcript modulates expression of the
cyclic-di-AMP hydrolase GdpP in Bacillus subtilis.";
Microbiology 158:2732-2741(2012).
[8]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=168 / YB886 / BG214;
PubMed=25616256; DOI=10.1016/j.dnarep.2014.12.007;
Gandara C., Alonso J.C.;
"DisA and c-di-AMP act at the intersection between DNA-damage response
and stress homeostasis in exponentially growing Bacillus subtilis
cells.";
DNA Repair 27:1-8(2015).
[9]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=168;
PubMed=26240071; DOI=10.1128/JB.00564-15;
Gundlach J., Mehne F.M., Herzberg C., Kampf J., Valerius O.,
Kaever V., Stuelke J.;
"An essential poison: synthesis and degradation of cyclic di-AMP in
Bacillus subtilis.";
J. Bacteriol. 197:3265-3274(2015).
-!- FUNCTION: Has phosphodiesterase (PDE) activity against cyclic-di-
AMP (c-di-AMP) and to a much lesser extent against cyclic-di-GMP
(c-di-GMP) in the DHH/DHHA1 domains (PubMed:19901023,
PubMed:21257773). Also has ATPase activity, probably via the GGDEF
domain (PubMed:19901023, PubMed:21257773). Overexpression leads to
increased sensitivity to methyl methanesulfonate (MMS) and
H(2)O(2) (PubMed:25616256). Overexpression leads to extreme
sensitivity to the beta-lactam antibiotic cefuroxime (CEF),
probably dependent on PDE activity (PubMed:22211522). May monitor
cellular heme or NO levels (PubMed:21257773). In B.subtilis c-di-
AMP is a second messenger that mediates growth, DNA repair and
cell wall homeostasis; it is toxic when present in excess
(PubMed:26240071). {ECO:0000269|PubMed:19901023,
ECO:0000269|PubMed:21257773, ECO:0000269|PubMed:22211522,
ECO:0000269|PubMed:25616256, ECO:0000269|PubMed:26240071}.
-!- CATALYTIC ACTIVITY: Cyclic di-3',5'-adenylate + H(2)O = 5'-
phosphoadenylyl(3'->5')adenosine. {ECO:0000269|PubMed:19901023}.
-!- COFACTOR:
Name=heme b; Xref=ChEBI:CHEBI:60344;
Evidence={ECO:0000269|PubMed:21257773};
Note=Binds 1 heme (probably heme b) per subunit, probably hexa-
coordinated, which inhibits PDE and ATPase. The Fe(2+) binds
CN(-), CO and NO. {ECO:0000269|PubMed:21257773};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:19901023};
Note=ATPase activity (residues 84-303) prefers Mg(2+) over Mn(2+).
{ECO:0000269|PubMed:19901023};
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:19901023};
Note=For phosphodiesterase activity (residues 84-695), probably
binds 2 Mn(2+) per subunit, can also use Co(2+), Mg(2+) or Ni(2+).
{ECO:0000269|PubMed:19901023};
-!- ACTIVITY REGULATION: Phosphodiesterase (PDE) inhibited by Zn(2+),
Ca(2+) inhibits in the presence of Mg(2+) but not Mn(2+); c-di-AMP
PDE activity is competitively inhibited by ppGpp
(PubMed:19901023). Heme binding (by Fe(2+) or Fe(3+) heme)
inhibits PDE, activity is partially restored by KCN or NO only for
Fe(2+) heme (PubMed:21257773). Binding of NO to Fe(2+) heme
switches from hexa- to pentacoordination (PubMed:21257773). Heme
binding inhibits the ATPase activity (PubMed:21257773).
{ECO:0000269|PubMed:19901023, ECO:0000269|PubMed:21257773}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.3 uM for c-di-AMP {ECO:0000269|PubMed:19901023};
KM=349 uM for c-di-GMP {ECO:0000269|PubMed:19901023};
KM=0.9 mM for ATP {ECO:0000269|PubMed:19901023};
Note=Phosphodiesterase kcat 0.55 for c-di-AMP, 0.23 for c-di-
GMP, tested for a construct expressing residues 84-695, a
shorter construct (residues 150-695) has a 10-fold decreased
kcat for both substrates. ATPase kcat 0.59.
{ECO:0000269|PubMed:19901023};
pH dependence:
Optimum pH is 8.5-9.2 (for a construct expressing residues 84-
695). {ECO:0000269|PubMed:19901023};
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255,
ECO:0000269|PubMed:21566650}; Multi-pass membrane protein
{ECO:0000255}. Note=After 3.5 hours of sporulation is present in a
punctate pattern associated with the cell membrane. Does not co-
localize with c-di-AMP synthase DisA.
{ECO:0000269|PubMed:21566650}.
-!- DEVELOPMENTAL STAGE: Expressed at low levels at the onset of
sporulation, it rises during sporulation (at protein level).
{ECO:0000269|PubMed:21566650}.
-!- INDUCTION: Probably transcribed under control of the sigma A
factor (sigA), protein levels are negatively regulated by an
antisense RNA (PubMed:22956758). {ECO:0000269|PubMed:22956758}.
-!- DOMAIN: Has a GGDEF domain (residues 173-310) preceded by a PAS-
like domain (residues 84-149) which together have ATPase activity,
followed by a region with a DHH (339-496) and a DHHA1 (591-646)
domain (PubMed:19901023). The combined GGDEF, DHH and DHHA1
domains have c-di-AMP phosphodiesterase activity (residues 150-
659) that is 10-fold enhanced by inclusion of the PAS-like domain
(84-149); PDE activity may only require the DHH/DHHA1 domains
(PubMed:19901023). The PAS-like domain is important for heme b-
binding (PubMed:21257773). {ECO:0000269|PubMed:19901023,
ECO:0000269|PubMed:21257773}.
-!- DISRUPTION PHENOTYPE: Increased resistance to acid stress,
increased sporulation efficiency following DNA damage (by
nalidixic acid) (PubMed:19901023). Increases c-di-AMP levels in
mid-exponential phase from about 3.8 uM to about 4.3 uM in strain
BG214 (PubMed:25616256). Increased levels of c-di-AMP 4-fold
during sporulation (PubMed:21566650). Insertion mutations in this
gene partially restore antibiotic resistance to the beta-lactam
antibiotic cefuroxime (CEF) in a sigM deletion mutant
(PubMed:22211522). Decreased sensitivity to MMS and H(2)O(2)
(PubMed:25616256). In strain 168 grown in minimal medium and
glutamate, 2.2-fold increase in c-di-AMP levels while a double
pgpH-gdpP mutant has 4.2-fold increased levels of in c-di-AMP;
double mutants die on solid medium after 2 days (PubMed:26240071).
{ECO:0000269|PubMed:19901023, ECO:0000269|PubMed:21566650,
ECO:0000269|PubMed:22211522, ECO:0000269|PubMed:25616256,
ECO:0000269|PubMed:26240071}.
-!- SIMILARITY: Belongs to the GdpP/PdeA phosphodiesterase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; D26185; BAA05182.1; -; Genomic_DNA.
EMBL; AL009126; CAB16088.1; -; Genomic_DNA.
PIR; S65976; S65976.
RefSeq; NP_391931.1; NC_000964.3.
RefSeq; WP_003242517.1; NZ_JNCM01000034.1.
ProteinModelPortal; P37484; -.
SMR; P37484; -.
STRING; 224308.Bsubs1_010100021861; -.
PaxDb; P37484; -.
PRIDE; P37484; -.
DNASU; 937816; -.
EnsemblBacteria; CAB16088; CAB16088; BSU40510.
GeneID; 937816; -.
KEGG; bsu:BSU40510; -.
PATRIC; fig|224308.179.peg.4385; -.
eggNOG; ENOG4105BZR; Bacteria.
eggNOG; COG3887; LUCA.
HOGENOM; HOG000112075; -.
OMA; YLEPYAS; -.
PhylomeDB; P37484; -.
BioCyc; BSUB:BSU40510-MONOMER; -.
Proteomes; UP000001570; Chromosome.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
InterPro; IPR001667; DDH_dom.
InterPro; IPR038763; DHH_sf.
InterPro; IPR003156; DHHA1_dom.
InterPro; IPR014528; GdpP/PdeA.
InterPro; IPR000160; GGDEF_dom.
Pfam; PF01368; DHH; 1.
Pfam; PF02272; DHHA1; 1.
PIRSF; PIRSF026583; YybT; 1.
SMART; SM00267; GGDEF; 1.
SUPFAM; SSF64182; SSF64182; 1.
PROSITE; PS50887; GGDEF; 1.
1: Evidence at protein level;
Cell membrane; Complete proteome; Heme; Hydrolase; Iron; Manganese;
Membrane; Metal-binding; Reference proteome; Sporulation;
Transmembrane; Transmembrane helix.
CHAIN 1 659 Cyclic-di-AMP phosphodiesterase GdpP.
/FTId=PRO_0000050071.
TOPO_DOM 1 8 Cytoplasmic.
{ECO:0000305|PubMed:19901023}.
TRANSMEM 9 29 Helical. {ECO:0000255}.
TRANSMEM 30 50 Helical. {ECO:0000255}.
TOPO_DOM 51 659 Cytoplasmic.
{ECO:0000305|PubMed:19901023}.
DOMAIN 173 301 GGDEF. {ECO:0000255|PROSITE-
ProRule:PRU00095}.
REGION 84 149 PAS-like domain, required for heme-
binding. {ECO:0000269|PubMed:21257773,
ECO:0000303|PubMed:19901023}.
REGION 339 496 DHH domain.
{ECO:0000269|PubMed:19901023}.
REGION 591 646 DHHA1 domain.
{ECO:0000269|PubMed:19901023}.
METAL 345 345 Manganese 1.
{ECO:0000305|PubMed:19901023}.
METAL 349 349 Manganese 1.
{ECO:0000305|PubMed:19901023}.
METAL 351 351 Manganese 2.
{ECO:0000305|PubMed:19901023}.
METAL 420 420 Manganese 1.
{ECO:0000305|PubMed:19901023}.
METAL 420 420 Manganese 2.
{ECO:0000305|PubMed:19901023}.
METAL 444 444 Manganese 2.
{ECO:0000305|PubMed:19901023}.
METAL 499 499 Manganese 2.
{ECO:0000305|PubMed:19901023}.
MUTAGEN 183 183 D->A: 5% ATPase activity.
{ECO:0000269|PubMed:19901023}.
MUTAGEN 225 225 E->A: 5% ATPase activity.
{ECO:0000269|PubMed:19901023}.
MUTAGEN 291 291 R->A: 5% ATPase activity.
{ECO:0000269|PubMed:19901023}.
MUTAGEN 420 420 D->A: Loss of phosphodiesterase activity,
does not confer antibiotic sensitivity
when overexpressed.
{ECO:0000269|PubMed:19901023,
ECO:0000269|PubMed:22211522}.
SEQUENCE 659 AA; 74325 MW; FD325C28A10EB14B CRC64;
MPSFYEKPLF RYPIYALIAL SIITILISFY FNWILGTVEV LLLAVILFFI KRADSLIRQE
IDAYISTLSY RLKKVGEEAL MEMPIGIMLF NDQYYIEWAN PFLSSCFNES TLVGRSLYDT
CESVVPLIKQ EVESETVTLN DRKFRVVIKR DERLLYFFDV TEQIQIEKLY ENERTVLAYI
FLDNYDDVTQ GLDDQTRSTM NSQVTSLLNA WAQEYGIFLK RTSSERFIAV LNEHILTELE
NSKFSILDEV REKTSFDGVA LTLSVGVGAS VSSLKELGDL AQSSLDLALG RGGDQVAIKL
PNGKVKFYGG KTNPMEKRTR VRARVISHAL KEIVTESSNV IIMGHKFPDM DSIGAAIGIL
KVAQANNKDG FIVIDPNQIG SSVQRLIGEI KKYEELWSRF ITPEEAMEIS NDDTLLVIVD
THKPSLVMEE RLVNKIEHIV VIDHHRRGEE FIRDPLLVYM EPYASSTAEL VTELLEYQPK
RLKINMIEAT ALLAGIIVDT KSFSLRTGSR TFDAASYLRA KGADTVLVQK FLKETVDSYI
KRAKLIQHTV LYKDNIAIAS LPENEEEYFD QVLIAQAADS LLSMSEVEAS FAVARRDEQT
VCISARSLGE VNVQIIMEAL EGGGHLTNAA TQLSGISVSE ALERLKHAID EYFEGGVQR


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