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Cyclic diguanosine monophosphate-binding protein PA4608 (c-di-GMP-binding protein PA4608) (Pilz domain-containing protein PA4608)

 CDGBP_PSEAE             Reviewed;         125 AA.
Q9HVI1;
24-JUL-2013, integrated into UniProtKB/Swiss-Prot.
01-MAR-2001, sequence version 1.
22-NOV-2017, entry version 90.
RecName: Full=Cyclic diguanosine monophosphate-binding protein PA4608 {ECO:0000303|PubMed:17096419, ECO:0000303|PubMed:21280119, ECO:0000303|PubMed:21310957};
Short=c-di-GMP-binding protein PA4608 {ECO:0000303|PubMed:17096419, ECO:0000303|PubMed:21280119, ECO:0000303|PubMed:21310957};
AltName: Full=Pilz domain-containing protein PA4608 {ECO:0000303|PubMed:17096419, ECO:0000303|PubMed:21280119, ECO:0000303|PubMed:21310957};
OrderedLocusNames=PA4608;
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] {ECO:0000312|EMBL:AAG07996.1}
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] {ECO:0000305, ECO:0000312|PDB:1YWU}
STRUCTURE BY NMR (APO-FORM), FUNCTION, SUBUNIT, DOMAIN, AND C-DI-GMP
BINDING.
STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 /
1C / PRS 101 / PAO1 {ECO:0000269|PubMed:17096419};
PubMed=17096419; DOI=10.1002/prot.21199;
Ramelot T.A., Yee A., Cort J.R., Semesi A., Arrowsmith C.H.,
Kennedy M.A.;
"NMR structure and binding studies confirm that PA4608 from
Pseudomonas aeruginosa is a PilZ domain and a c-di-GMP binding
protein.";
Proteins 66:266-271(2007).
[3] {ECO:0000305, ECO:0000312|PDB:2L74}
STRUCTURE BY NMR IN COMPLEX WITH C-DI-GMP (HOLO-FORM), FUNCTION,
SUBUNIT, DOMAIN, AND MOTIF.
PubMed=21310957; DOI=10.1074/jbc.M110.209007;
Habazettl J., Allan M.G., Jenal U., Grzesiek S.;
"Solution structure of the PilZ domain protein PA4608 complex with
cyclic di-GMP identifies charge clustering as molecular readout.";
J. Biol. Chem. 286:14304-14314(2011).
[4] {ECO:0000305}
STRUCTURE BY NMR, FUNCTION, SUBUNIT, DOMAIN, MOTIF, SITE, AND
MUTAGENESIS OF ARG-9; ARG-13 AND GLY-40.
PubMed=21280119; DOI=10.1002/pro.557;
Shin J.S., Ryu K.S., Ko J., Lee A., Choi B.S.;
"Structural characterization reveals that a PilZ domain protein
undergoes substantial conformational change upon binding to cyclic
dimeric guanosine monophosphate.";
Protein Sci. 20:270-277(2011).
-!- FUNCTION: Binds the second messenger bis-(3'-5') cyclic dimeric
guanosine monophosphate (c-di-GMP). Can bind two c-di-GMP
molecules per monomer. May play a role in bacterial second-
messenger regulated processes. Binding to c-di-GMP induces a
conformational change of the C- and N-termini resulting in the
exposure of a highly negative surface on one side of the protein
to a possible effector protein. {ECO:0000269|PubMed:17096419,
ECO:0000269|PubMed:21280119, ECO:0000269|PubMed:21310957}.
-!- SUBUNIT: Monomer in both c-di-GMP-bound and free forms.
{ECO:0000269|PubMed:17096419, ECO:0000269|PubMed:21280119,
ECO:0000269|PubMed:21310957}.
-!- DOMAIN: Consists of a six-stranded anti-parallel beta-barrel core
structure with an unstructured N-terminus in apo-form and a C-
terminal alpha helix. In the holo-form the C-terminal helix is
displaced by the ligand, thereby opening one side of the beta-
barrel as a binding site, and the N-terminus containing the RXXXR
motif wraps around the ligand and in turn ties the C-terminal
helix in a loose conformation. The structural rearrangement upon
ligand binding creates a significant change in surface charge
distribution. {ECO:0000269|PubMed:17096419,
ECO:0000269|PubMed:21280119, ECO:0000269|PubMed:21310957}.
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EMBL; AE004091; AAG07996.1; -; Genomic_DNA.
PIR; H83068; H83068.
RefSeq; NP_253298.1; NC_002516.2.
RefSeq; WP_003094864.1; NC_002516.2.
PDB; 1YWU; NMR; -; A=1-125.
PDB; 2L74; NMR; -; A=1-125.
PDB; 5XLY; X-ray; 1.76 A; B=1-125.
PDBsum; 1YWU; -.
PDBsum; 2L74; -.
PDBsum; 5XLY; -.
ProteinModelPortal; Q9HVI1; -.
SMR; Q9HVI1; -.
STRING; 208964.PA4608; -.
PaxDb; Q9HVI1; -.
PRIDE; Q9HVI1; -.
DNASU; 881102; -.
EnsemblBacteria; AAG07996; AAG07996; PA4608.
GeneID; 881102; -.
KEGG; pae:PA4608; -.
PATRIC; fig|208964.12.peg.4823; -.
PseudoCAP; PA4608; -.
HOGENOM; HOG000283213; -.
OMA; GFVCRHI; -.
PhylomeDB; Q9HVI1; -.
EvolutionaryTrace; Q9HVI1; -.
Proteomes; UP000002438; Chromosome.
GO; GO:0005622; C:intracellular; IEA:GOC.
GO; GO:0035438; F:cyclic-di-GMP binding; IDA:UniProtKB.
GO; GO:0019932; P:second-messenger-mediated signaling; IDA:UniProtKB.
InterPro; IPR027021; C-di-GMP_BP_PA4608.
InterPro; IPR009875; PilZ_domain.
Pfam; PF07238; PilZ; 1.
PIRSF; PIRSF028141; C-di-GMP_BP_PA4608; 1.
1: Evidence at protein level;
3D-structure; c-di-GMP; Complete proteome; Nucleotide-binding;
Reference proteome.
CHAIN 1 125 Cyclic diguanosine monophosphate-binding
protein PA4608.
/FTId=PRO_0000423181.
DOMAIN 7 103 PilZ. {ECO:0000255}.
NP_BIND 6 13 c-di-GMP. {ECO:0000269|PubMed:21310957}.
MOTIF 9 13 RXXXR motif; surrounds the surface of the
c-di-GMP binding site.
{ECO:0000269|PubMed:21280119,
ECO:0000269|PubMed:21310957}.
MOTIF 35 40 DXSXXG motif; surrounds the surface of
the c-di-GMP binding site.
{ECO:0000269|PubMed:21280119,
ECO:0000269|PubMed:21310957}.
BINDING 77 77 c-di-GMP. {ECO:0000269|PubMed:21310957}.
SITE 40 40 Important for c-di-GMP binding.
MUTAGEN 9 9 R->A: Abolishes c-di-GMP binding.
{ECO:0000269|PubMed:21280119}.
MUTAGEN 13 13 R->A: Abolishes c-di-GMP binding.
{ECO:0000269|PubMed:21280119}.
MUTAGEN 40 40 G->A: Abolishes c-di-GMP binding.
{ECO:0000269|PubMed:21280119}.
TURN 3 6 {ECO:0000244|PDB:2L74}.
STRAND 9 11 {ECO:0000244|PDB:2L74}.
STRAND 19 24 {ECO:0000244|PDB:5XLY}.
STRAND 27 31 {ECO:0000244|PDB:5XLY}.
STRAND 33 37 {ECO:0000244|PDB:5XLY}.
STRAND 40 44 {ECO:0000244|PDB:5XLY}.
STRAND 57 63 {ECO:0000244|PDB:5XLY}.
TURN 64 66 {ECO:0000244|PDB:5XLY}.
STRAND 67 79 {ECO:0000244|PDB:5XLY}.
STRAND 82 91 {ECO:0000244|PDB:5XLY}.
HELIX 92 106 {ECO:0000244|PDB:5XLY}.
HELIX 109 120 {ECO:0000244|PDB:5XLY}.
TURN 121 123 {ECO:0000244|PDB:5XLY}.
SEQUENCE 125 AA; 14573 MW; AB6D8110967348B0 CRC64;
MSDQHDERRR FHRIAFDADS EILQGERRWE VLLHDVSLHG ILVGQPQDWN GDPQRPFEAR
LYLGLDVLIR MEISLAWARD GLLGFECQHI DLDSISHLRR LVELNLGDEE LLERELALLV
SAHDD


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