ID   CDPA_VIBCH              Reviewed;         829 AA.
AC   Q9KVL2;
DT   19-MAR-2014, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   03-AUG-2022, entry version 95.
DE   RecName: Full=Cyclic di-GMP phosphodiesterase CdpA;
DE            Short=c-di-GMP PDE;
DE            EC=3.1.4.52;
GN   Name=cdpA; OrderedLocusNames=VC_0130;
OS   Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=243277;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX   PubMed=10952301; DOI=10.1038/35020000;
RA   Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA   Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA   Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA   Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA   Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA   Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT   "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT   cholerae.";
RL   Nature 406:477-483(2000).
RN   [2]
RP   FUNCTION, CATALYTIC ACTIVITY, GENE NAME, INDUCTION, DOMAIN, DISRUPTION
RP   PHENOTYPE, AND MUTAGENESIS OF 493-GLY--GLU-496.
RC   STRAIN=El Tor C6709 / Serotype O1;
RX   PubMed=18227161; DOI=10.1128/iai.01337-07;
RA   Tamayo R., Schild S., Pratt J.T., Camilli A.;
RT   "Role of cyclic di-GMP during el tor biotype Vibrio cholerae infection:
RT   characterization of the in vivo-induced cyclic di-GMP phosphodiesterase
RT   CdpA.";
RL   Infect. Immun. 76:1617-1627(2008).
CC   -!- FUNCTION: Phosphodiesterase (PDE) that catalyzes the hydrolysis of
CC       cyclic diguanylate (c-di-GMP). Is involved in the modulation of
CC       intracellular c-di-GMP levels. Cyclic-di-GMP is a second messenger
CC       which positively regulates biofilm formation and negatively regulates
CC       virulence in V.cholerae, and is proposed to play an important role in
CC       the transition from persistence in the environment to survival in the
CC       host. CdpA functions as a repressor of biofilm formation but has no
CC       effect on colonization of the infant mouse small intestine. Does not
CC       possess diguanylate cyclase (DGC) activity, due to its inactive
CC       degenerate GGDEF domain. {ECO:0000269|PubMed:18227161}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=cyclic di-3',5'-guanylate + H2O = 5'-
CC         phosphoguanylyl(3'->5')guanosine + H(+); Xref=Rhea:RHEA:24902,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:58754,
CC         ChEBI:CHEBI:58805; EC=3.1.4.52;
CC         Evidence={ECO:0000269|PubMed:18227161};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC   -!- INDUCTION: Is up-regulated during biofilm formation, and is also
CC       induced during a late stage of infection of the host. However, cdpA
CC       expression is not regulated by c-di-GMP concentration.
CC       {ECO:0000269|PubMed:18227161}.
CC   -!- DOMAIN: The EAL domain is required for c-di-GMP PDE activity, and the
CC       degenerate GGDEF domain is required for full PDE activity of the EAL
CC       domain (PubMed:18227161). The GG(D/E)EF motif in CdpA is degenerate,
CC       having the sequence GVGEW. {ECO:0000269|PubMed:18227161}.
CC   -!- DISRUPTION PHENOTYPE: Cells lacking this gene have a level of c-di-GMP
CC       almost four-fold higher than that of the respective parent strain.
CC       Disruption of this gene also results in increased biofilm formation.
CC       {ECO:0000269|PubMed:18227161}.
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DR   EMBL; AE003852; AAF93307.1; -; Genomic_DNA.
DR   PIR; C82361; C82361.
DR   RefSeq; NP_229788.1; NC_002505.1.
DR   RefSeq; WP_000495585.1; NZ_LT906614.1.
DR   AlphaFoldDB; Q9KVL2; -.
DR   SMR; Q9KVL2; -.
DR   STRING; 243277.VC_0130; -.
DR   PRIDE; Q9KVL2; -.
DR   DNASU; 2614885; -.
DR   EnsemblBacteria; AAF93307; AAF93307; VC_0130.
DR   GeneID; 57741373; -.
DR   KEGG; vch:VC_0130; -.
DR   PATRIC; fig|243277.26.peg.121; -.
DR   eggNOG; COG2199; Bacteria.
DR   eggNOG; COG2200; Bacteria.
DR   eggNOG; COG3287; Bacteria.
DR   HOGENOM; CLU_000445_75_2_6; -.
DR   OMA; FEHNTDI; -.
DR   BioCyc; VCHO:VC0130-MON; -.
DR   Proteomes; UP000000584; Chromosome 1.
DR   GO; GO:0071111; F:cyclic-guanylate-specific phosphodiesterase activity; IEA:UniProtKB-EC.
DR   CDD; cd01948; EAL; 1.
DR   Gene3D; 3.20.20.450; -; 1.
DR   Gene3D; 3.30.70.270; -; 1.
DR   InterPro; IPR001633; EAL_dom.
DR   InterPro; IPR035919; EAL_sf.
DR   InterPro; IPR019494; FIST_C.
DR   InterPro; IPR013702; FIST_domain_N.
DR   InterPro; IPR000160; GGDEF_dom.
DR   InterPro; IPR029787; Nucleotide_cyclase.
DR   InterPro; IPR043128; Rev_trsase/Diguanyl_cyclase.
DR   Pfam; PF00563; EAL; 1.
DR   Pfam; PF08495; FIST; 1.
DR   Pfam; PF10442; FIST_C; 1.
DR   Pfam; PF00990; GGDEF; 1.
DR   SMART; SM00052; EAL; 1.
DR   SMART; SM00897; FIST; 1.
DR   SMART; SM01204; FIST_C; 1.
DR   SMART; SM00267; GGDEF; 1.
DR   SUPFAM; SSF141868; SSF141868; 1.
DR   SUPFAM; SSF55073; SSF55073; 1.
DR   PROSITE; PS50883; EAL; 1.
PE   1: Evidence at protein level;
KW   c-di-GMP; Hydrolase; Magnesium; Reference proteome.
FT   CHAIN           1..829
FT                   /note="Cyclic di-GMP phosphodiesterase CdpA"
FT                   /id="PRO_0000425960"
FT   DOMAIN          593..829
FT                   /note="EAL"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00074"
FT   REGION          419..480
FT                   /note="Degenerate GGDEF domain"
FT   MUTAGEN         493..496
FT                   /note="GVGE->AVGA: Reduction in PDE activity."
FT                   /evidence="ECO:0000269|PubMed:18227161"
SQ   SEQUENCE   829 AA;  94055 MW;  F3A6FCC77AD5BE3B CRC64;
     MFTVSRLIPD LASANQVLET MDLPHGQSIL VQIFSPLSRE HVVQLARLIR SRHPQACLLG
     CSTEEVIFQG EVHHQVTLLQ ITVFEQTYLS RAVVDYSDDE AADAERLARQ LELTSMSRAV
     VCFSWQMDTL QVARFALRDT QGAPVPVAGG AAKQTPSGRW VLLDEACYQN ASVAIALHGE
     ALYVETGGYT EWQPVGRTYR VTAVEGDRVL RLDDEPIEAI YQRNLGAQAD LPHDWLISFP
     LMKGECRHQD LYLPLGLAEE GGLRFNRPLA LQDEVRFCFD HPSLTLERVY LTAQQLQAKQ
     CQQVWVFNCA LRLNFMHENH ELQPLQAVAP TDGCYCWGEL LYEHGQQQVM HHSMTFLALR
     EGAVRDDLVP IPLPSYPEGM TSPLFNLIRH AFHDLDAMTD NLAQQIRAQT SLLTASYRRD
     RRTGLPNRVV LRERLANFAA NEHLIALKVT NFNQINEKYG YPVGDKLLRD LSEQFQVFLD
     QKLAGQSGLY AIGVGEWATV FRAKLDGKSI HSHFYQFVEQ LEHVNFEPYG LPNVDYLSIS
     LCAGLVSQGD FAEHSPDELL LRAIEARRYA FNNNHHFCNA ARLKVQESVR QERLNWLSRV
     SRAVVRDDVV VYAQPICQAR SHIVASYECL VRIEDEGEII LPGNFLPIIT DTHLYTRLSR
     QMITHTFNMM RHRPEAFSIN LSPQDLMSER TLQHLEAAIK SVADPARVGL EVLESEQIKD
     YGRMIEVCNH FRTLGATIIV DDFGSGYSNI DEIVKLEPQV IKLDGSLIRN IDQDVKQRRI
     AEQLVKLCQV LNAKTVAEFV HNQTVCRISE DMGVDYLQGY FLGRPSRLG