CDPD1_PSEAE
ID CDPD1_PSEAE Reviewed; 414 AA.
AC Q9HWS0;
DT 05-JUL-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 107.
DE RecName: Full=Cyclic di-GMP phosphodiesterase PA4108 {ECO:0000303|PubMed:19170727};
DE EC=3.1.4.- {ECO:0000269|PubMed:24066157};
GN OrderedLocusNames=PA4108 {ECO:0000312|EMBL:AAG07495.1};
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [2]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=19170727; DOI=10.1111/j.1462-2920.2008.01842.x;
RA Ryan R.P., Lucey J., O'Donovan K., McCarthy Y., Yang L., Tolker-Nielsen T.,
RA Dow J.M.;
RT "HD-GYP domain proteins regulate biofilm formation and virulence in
RT Pseudomonas aeruginosa.";
RL Environ. Microbiol. 11:1126-1136(2009).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBUNIT.
RX PubMed=24066157; DOI=10.1371/journal.pone.0074920;
RA Stelitano V., Giardina G., Paiardini A., Castiglione N., Cutruzzola F.,
RA Rinaldo S.;
RT "C-di-GMP hydrolysis by Pseudomonas aeruginosa HD-GYP phosphodiesterases:
RT analysis of the reaction mechanism and novel roles for pGpG.";
RL PLoS ONE 8:E74920-E74920(2013).
CC -!- FUNCTION: Phosphodiesterase (PDE) that catalyzes the hydrolysis of
CC cyclic diguanylate (c-di-GMP) to GMP (PubMed:19170727,
CC PubMed:24066157). Hydrolyzes c-di-GMP to GMP in a two-step reaction,
CC via the linear intermediate 5'-phosphoguanylyl(3'->5')guanosine (pGpG).
CC In vitro, can use pGpG as an alternative substrate and hydrolyze it
CC into GMP (PubMed:24066157). Acts in regulation of motility, synthesis
CC of virulence determinants and biofilm architecture (PubMed:19170727).
CC {ECO:0000269|PubMed:19170727, ECO:0000269|PubMed:24066157}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=cyclic di-3',5'-guanylate + 2 H2O = 2 GMP + 2 H(+);
CC Xref=Rhea:RHEA:52928, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:58115, ChEBI:CHEBI:58805;
CC Evidence={ECO:0000269|PubMed:24066157};
CC -!- ACTIVITY REGULATION: Activated by Mg(2+) and Mn(2+).
CC {ECO:0000269|PubMed:24066157}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=20 uM for c-di-GMP {ECO:0000269|PubMed:24066157};
CC KM=30 uM for pGpG {ECO:0000269|PubMed:24066157};
CC Note=kcat is 0.00015 sec(-1). {ECO:0000269|PubMed:24066157};
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:24066157};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius.
CC {ECO:0000269|PubMed:24066157};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:24066157}.
CC -!- DISRUPTION PHENOTYPE: Disruption mutant has increased levels of cyclic
CC di-GMP. Mutation leads to reduction in both swarming and twitching
CC motility, to a decrease in pyocyanine production, to a reduction in the
CC extracellular levels of the ExoS effector, and a reduction in
CC virulence. It produces a flatter biofilm.
CC {ECO:0000269|PubMed:19170727}.
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DR EMBL; AE004091; AAG07495.1; -; Genomic_DNA.
DR PIR; D83132; D83132.
DR RefSeq; NP_252797.1; NC_002516.2.
DR RefSeq; WP_003113015.1; NZ_QZGE01000013.1.
DR AlphaFoldDB; Q9HWS0; -.
DR SMR; Q9HWS0; -.
DR STRING; 287.DR97_3764; -.
DR PaxDb; Q9HWS0; -.
DR EnsemblBacteria; AAG07495; AAG07495; PA4108.
DR GeneID; 877982; -.
DR KEGG; pae:PA4108; -.
DR PATRIC; fig|208964.12.peg.4304; -.
DR PseudoCAP; PA4108; -.
DR HOGENOM; CLU_000445_92_1_6; -.
DR InParanoid; Q9HWS0; -.
DR OMA; HTIYGYQ; -.
DR PhylomeDB; Q9HWS0; -.
DR BioCyc; PAER208964:G1FZ6-4180-MON; -.
DR BRENDA; 3.1.4.52; 5087.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0071111; F:cyclic-guanylate-specific phosphodiesterase activity; IDA:PseudoCAP.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:2000147; P:positive regulation of cell motility; IMP:PseudoCAP.
DR GO; GO:1900231; P:regulation of single-species biofilm formation on inanimate substrate; IMP:PseudoCAP.
DR CDD; cd00077; HDc; 1.
DR InterPro; IPR021812; DUF3391.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR037522; HD_GYP_dom.
DR InterPro; IPR006675; HDIG_dom.
DR Pfam; PF11871; DUF3391; 1.
DR Pfam; PF01966; HD; 1.
DR SMART; SM00471; HDc; 1.
DR TIGRFAMs; TIGR00277; HDIG; 1.
DR PROSITE; PS51832; HD_GYP; 1.
PE 1: Evidence at protein level;
KW c-di-GMP; Hydrolase; Metal-binding; Reference proteome.
FT CHAIN 1..414
FT /note="Cyclic di-GMP phosphodiesterase PA4108"
FT /id="PRO_0000440636"
FT DOMAIN 133..330
FT /note="HD-GYP"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01176"
FT BINDING 160
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9HV27"
FT BINDING 192
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9HV27"
FT BINDING 193
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:Q9HV27"
FT BINDING 193
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9HV27"
FT BINDING 221
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9HV27"
FT BINDING 246
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9HV27"
FT BINDING 247
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:Q9HV27"
SQ SEQUENCE 414 AA; 45419 MW; D17B47BCC6A42786 CRC64;
MLKRIPVTQL RLGMFVQSLC GSWLDHPFWK RGGFLLDSQA DLQRLRESAV KEVWIDASKG
LDLPEEAAVS AAAVLPVTMP AGPSPARVAL EEEIRHAALL CSRAKAAVVS MFRDARMGQA
IDTAHASDLV DEISASVLRH PNALLSLVRL KTSDEYTYMH SVAVCALMIA LARQLELPDP
LVREAGLAGL LHDIGKMAVP DPILNKPGKL TDPEFGLVRR HPQNGARMLL DCRQVSALVV
DVCLHHHERI DGTGYPFGLA QEQISLLARM GAVCDVYDAI TSDRPYKKGW NAAEAIRRMA
EWNGHFDPQV FRAFVKAVGI YPVGALVRLE SGRLGVVLEQ HGRSLLTPRV KVFFSARSKV
PIPQQVVDLG RAGQTDRIVG FEPAEAWNFR NLDEMWTGLA KSTGSYFDAG TGNP
