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Cyclic di-GMP phosphodiesterase PA4781 (EC 3.1.4.-)

 CDPD2_PSEAE             Reviewed;         393 AA.
Q9HV27;
05-JUL-2017, integrated into UniProtKB/Swiss-Prot.
01-MAR-2001, sequence version 1.
25-OCT-2017, entry version 109.
RecName: Full=Cyclic di-GMP phosphodiesterase PA4781 {ECO:0000303|PubMed:19170727};
EC=3.1.4.- {ECO:0000269|PubMed:24066157};
OrderedLocusNames=PA4781 {ECO:0000312|EMBL:AAG08167.1};
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 /
JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
Pseudomonadaceae; Pseudomonas.
NCBI_TaxID=208964;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
1C / PRS 101 / PAO1;
PubMed=10984043; DOI=10.1038/35023079;
Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T.,
Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
"Complete genome sequence of Pseudomonas aeruginosa PAO1, an
opportunistic pathogen.";
Nature 406:959-964(2000).
[2]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
1C / PRS 101 / PAO1;
PubMed=19170727; DOI=10.1111/j.1462-2920.2008.01842.x;
Ryan R.P., Lucey J., O'Donovan K., McCarthy Y., Yang L.,
Tolker-Nielsen T., Dow J.M.;
"HD-GYP domain proteins regulate biofilm formation and virulence in
Pseudomonas aeruginosa.";
Environ. Microbiol. 11:1126-1136(2009).
[3]
FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL
PROPERTIES, SUBUNIT, PHOSPHORYLATION, AND MUTAGENESIS OF GLU-314.
PubMed=24066157; DOI=10.1371/journal.pone.0074920;
Stelitano V., Giardina G., Paiardini A., Castiglione N.,
Cutruzzola F., Rinaldo S.;
"C-di-GMP hydrolysis by Pseudomonas aeruginosa HD-GYP
phosphodiesterases: analysis of the reaction mechanism and novel roles
for pGpG.";
PLoS ONE 8:E74920-E74920(2013).
[4] {ECO:0000244|PDB:4R8Z}
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF 151-368 IN COMPLEX WITH
NICKEL, SUBUNIT, AND DOMAIN.
PubMed=25691523; DOI=10.1128/JB.02606-14;
Rinaldo S., Paiardini A., Stelitano V., Brunotti P., Cervoni L.,
Fernicola S., Protano C., Vitali M., Cutruzzola F., Giardina G.;
"Structural basis of functional diversification of the HD-GYP domain
revealed by the Pseudomonas aeruginosa PA4781 protein, which displays
an unselective bimetallic binding site.";
J. Bacteriol. 197:1525-1535(2015).
-!- FUNCTION: Phosphodiesterase (PDE) that catalyzes the hydrolysis of
cyclic diguanylate (c-di-GMP) to GMP (PubMed:19170727,
PubMed:24066157). Hydrolyzes c-di-GMP to GMP in a two-step
reaction, via the linear intermediate 5'-
phosphoguanylyl(3'->5')guanosine (pGpG). In vitro, can use pGpG as
an alternative substrate and hydrolyze it into GMP
(PubMed:24066157). Acts in regulation of motility, synthesis of
virulence determinants and biofilm architecture (PubMed:19170727).
May act preferentially as a pGpG binding protein
(PubMed:24066157). {ECO:0000269|PubMed:19170727,
ECO:0000269|PubMed:24066157}.
-!- CATALYTIC ACTIVITY: Cyclic di-3',5'-guanylate + 2 H(2)O = 2 GMP.
{ECO:0000269|PubMed:24066157}.
-!- ENZYME REGULATION: Phosphodiesterase activity is activated by
phosphorylation of the N-terminal regulatory domain.
Phosphorylation triggers a conformational change of the HD-GYP
domain, which renders the active site accessible.
{ECO:0000269|PubMed:24066157}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=119 uM for c-di-GMP {ECO:0000269|PubMed:24066157};
KM=27 uM for pGpG {ECO:0000269|PubMed:24066157};
Note=kcat is 0.0002 sec(-1). {ECO:0000269|PubMed:24066157};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24066157,
ECO:0000269|PubMed:25691523}.
-!- DOMAIN: Contains an unselective bimetallic binding site, with a
high-affinity site (H-site) and a low-affinity site (L-site).
Metal binding to the H-site triggers the binding to the L-site.
This bimetallic center may play a structural more than a catalytic
role. {ECO:0000269|PubMed:25691523}.
-!- PTM: Phosphorylated. {ECO:0000269|PubMed:24066157}.
-!- DISRUPTION PHENOTYPE: Disruption mutant has increased levels of
cyclic di-GMP. Mutation leads to reduction in both swarming and
twitching motility, to an increase in pyoverdine production, and a
reduction in virulence. It produces a biofilm with little
heterogeneity. {ECO:0000269|PubMed:19170727}.
-----------------------------------------------------------------------
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EMBL; AE004091; AAG08167.1; -; Genomic_DNA.
PIR; C83049; C83049.
RefSeq; NP_253469.1; NC_002516.2.
RefSeq; WP_003102241.1; NC_002516.2.
PDB; 4R8Z; X-ray; 2.20 A; A/B=151-368.
PDBsum; 4R8Z; -.
ProteinModelPortal; Q9HV27; -.
SMR; Q9HV27; -.
STRING; 208964.PA4781; -.
PaxDb; Q9HV27; -.
EnsemblBacteria; AAG08167; AAG08167; PA4781.
GeneID; 880075; -.
KEGG; pae:PA4781; -.
PATRIC; fig|208964.12.peg.5009; -.
PseudoCAP; PA4781; -.
eggNOG; ENOG4105DW3; Bacteria.
eggNOG; COG3437; LUCA.
HOGENOM; HOG000266481; -.
InParanoid; Q9HV27; -.
KO; K07814; -.
OMA; DNPRSRH; -.
PhylomeDB; Q9HV27; -.
Proteomes; UP000002438; Chromosome.
GO; GO:0005622; C:intracellular; IEA:GOC.
GO; GO:0071111; F:cyclic-guanylate-specific phosphodiesterase activity; IDA:PseudoCAP.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000160; P:phosphorelay signal transduction system; IEA:InterPro.
GO; GO:2000147; P:positive regulation of cell motility; IMP:PseudoCAP.
GO; GO:1900231; P:regulation of single-species biofilm formation on inanimate substrate; IMP:PseudoCAP.
CDD; cd00077; HDc; 1.
CDD; cd00156; REC; 1.
InterPro; IPR011006; CheY-like_superfamily.
InterPro; IPR003607; HD/PDEase_dom.
InterPro; IPR001789; Sig_transdc_resp-reg_receiver.
Pfam; PF00072; Response_reg; 1.
SMART; SM00471; HDc; 1.
SMART; SM00448; REC; 1.
SUPFAM; SSF52172; SSF52172; 1.
PROSITE; PS51832; HD_GYP; 1.
PROSITE; PS50110; RESPONSE_REGULATORY; 1.
1: Evidence at protein level;
3D-structure; c-di-GMP; Complete proteome; Hydrolase; Metal-binding;
Phosphoprotein; Reference proteome.
CHAIN 1 393 Cyclic di-GMP phosphodiesterase PA4781.
/FTId=PRO_0000440637.
DOMAIN 12 128 Response regulatory.
{ECO:0000255|PROSITE-ProRule:PRU00169}.
DOMAIN 155 366 HD-GYP. {ECO:0000255|PROSITE-
ProRule:PRU01176}.
METAL 180 180 Divalent metal cation 1.
{ECO:0000269|PubMed:25691523}.
METAL 220 220 Divalent metal cation 1.
{ECO:0000269|PubMed:25691523}.
METAL 221 221 Divalent metal cation 1.
{ECO:0000269|PubMed:25691523}.
METAL 221 221 Divalent metal cation 2.
{ECO:0000269|PubMed:25691523}.
METAL 249 249 Divalent metal cation 2.
{ECO:0000269|PubMed:25691523}.
METAL 281 281 Divalent metal cation 2.
{ECO:0000269|PubMed:25691523}.
METAL 282 282 Divalent metal cation 2.
{ECO:0000269|PubMed:25691523}.
MOD_RES 61 61 4-aspartylphosphate.
{ECO:0000255|PROSITE-ProRule:PRU00169}.
MUTAGEN 314 314 E->A: Increases affinity for c-di-GMP.
{ECO:0000269|PubMed:24066157}.
HELIX 153 169 {ECO:0000244|PDB:4R8Z}.
TURN 170 174 {ECO:0000244|PDB:4R8Z}.
HELIX 180 196 {ECO:0000244|PDB:4R8Z}.
HELIX 199 202 {ECO:0000244|PDB:4R8Z}.
HELIX 207 216 {ECO:0000244|PDB:4R8Z}.
HELIX 217 219 {ECO:0000244|PDB:4R8Z}.
HELIX 222 226 {ECO:0000244|PDB:4R8Z}.
HELIX 229 232 {ECO:0000244|PDB:4R8Z}.
HELIX 240 247 {ECO:0000244|PDB:4R8Z}.
HELIX 249 261 {ECO:0000244|PDB:4R8Z}.
HELIX 269 280 {ECO:0000244|PDB:4R8Z}.
STRAND 289 292 {ECO:0000244|PDB:4R8Z}.
HELIX 296 298 {ECO:0000244|PDB:4R8Z}.
HELIX 301 315 {ECO:0000244|PDB:4R8Z}.
HELIX 327 335 {ECO:0000244|PDB:4R8Z}.
TURN 339 341 {ECO:0000244|PDB:4R8Z}.
HELIX 344 363 {ECO:0000244|PDB:4R8Z}.
SEQUENCE 393 AA; 43629 MW; D2CD7F712E8F797E CRC64;
MESMLDRPEQ ELVLVVDDTP DNLLLMRELL EEQYRVRTAG SGPAGLRAAV EEPRPDLILL
DVNMPGMDGY EVCRRLKADP LTRDIPLMFL TARADRDDEQ QGLALGAVDY LGKPVSPPIV
LARVRTHLQL KANADFLRDK SEYLELEVRR RTRQLQQLQD AVIEALATLG DLRDNPRSRH
LPRIERYVRL LAEHLAAQRA FADELTPEAV DLLSKSALLH DIGKVAVPDR VLLNPGQLDA
ADTALLQGHT RAGRDALASA ERRLGQPSGF LRFARQIAYS HHERWDGRGF PEGLAGERIP
LAARIVALAD RYDELTSRHA YRPPLAHAEA VLLIQAGAGS EFDPRLVEAF VAVADAFAEV
ARRYADSAEA LDVEMQRLEQ AVAESIELTA PPA


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