ID   CLP_XANCP               Reviewed;         230 AA.
AC   P22260; Q9S6B5;
DT   01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT   11-JUL-2002, sequence version 2.
DT   27-MAR-2024, entry version 151.
DE   RecName: Full=CRP-like protein Clp;
DE   AltName: Full=Catabolite activation-like protein;
DE            Short=CAP-like;
GN   Name=clp; OrderedLocusNames=XCC0472;
OS   Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB
OS   528 / LMG 568 / P 25).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales;
OC   Xanthomonadaceae; Xanthomonas.
OX   NCBI_TaxID=190485;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 13951 / NCIB 11803 / NRRL B-1459;
RX   PubMed=2170330; DOI=10.1128/jb.172.10.5877-5883.1990;
RA   de Crecy-Lagard V., Glaser P., Lejeune P., Sismeiro O., Barber C.E.,
RA   Daniels M.J., Danchin A.;
RT   "A Xanthomonas campestris pv. campestris protein similar to catabolite
RT   activation factor is involved in regulation of phytopathogenicity.";
RL   J. Bacteriol. 172:5877-5883(1990).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=1322886; DOI=10.1128/jb.174.16.5457-5461.1992;
RA   Dong Q., Ebright R.H.;
RT   "DNA binding specificity and sequence of Xanthomonas campestris catabolite
RT   gene activator protein-like protein.";
RL   J. Bacteriol. 174:5457-5461(1992).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=Xc17;
RX   PubMed=11361081;
RA   Lee T.C., Chen S.T., Lee M.C., Chang C.M., Chen C.H., Weng S.F.,
RA   Tseng Y.H.;
RT   "The early stages of filamentous phage phiLf infection require the host
RT   transcription factor, Clp.";
RL   J. Mol. Microbiol. Biotechnol. 3:471-481(2001).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25;
RX   PubMed=12024217; DOI=10.1038/417459a;
RA   da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R.,
RA   Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr.,
RA   Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G.,
RA   Cannavan F., Cardozo J., Chambergo F., Ciapina L.P., Cicarelli R.M.B.,
RA   Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B.,
RA   Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F.,
RA   Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T.,
RA   Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A.,
RA   Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J.,
RA   Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M.,
RA   Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A.,
RA   Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A.,
RA   Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M.,
RA   Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P.;
RT   "Comparison of the genomes of two Xanthomonas pathogens with differing host
RT   specificities.";
RL   Nature 417:459-463(2002).
RN   [5]
RP   FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=Xc1;
RX   PubMed=17378922; DOI=10.1111/j.1365-2958.2007.05670.x;
RA   He Y.W., Ng A.Y., Xu M., Lin K., Wang L.H., Dong Y.H., Zhang L.H.;
RT   "Xanthomonas campestris cell-cell communication involves a putative
RT   nucleotide receptor protein Clp and a hierarchical signalling network.";
RL   Mol. Microbiol. 64:281-292(2007).
RN   [6]
RP   DNA-BINDING, AND ACTIVITY REGULATION.
RC   STRAIN=8004;
RX   PubMed=20008070; DOI=10.1128/jb.01253-09;
RA   Tao F., He Y.W., Wu D.H., Swarup S., Zhang L.H.;
RT   "The cyclic nucleotide monophosphate domain of Xanthomonas campestris
RT   global regulator Clp defines a new class of cyclic di-GMP effectors.";
RL   J. Bacteriol. 192:1020-1029(2010).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), DNA-BINDING, ACTIVITY REGULATION,
RP   SUBUNIT, DOMAIN, AND MUTAGENESIS OF ASP-70; GLU-99; ARG-150; ARG-154;
RP   ASP-162; VAL-165; ARG-166; ASP-170 AND ARG-195.
RC   STRAIN=Xc17;
RX   PubMed=20004667; DOI=10.1016/j.jmb.2009.11.076;
RA   Chin K.H., Lee Y.C., Tu Z.L., Chen C.H., Tseng Y.H., Yang J.M., Ryan R.P.,
RA   McCarthy Y., Dow J.M., Wang A.H., Chou S.H.;
RT   "The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking
RT   cell-cell signaling to virulence gene expression in Xanthomonas
RT   campestris.";
RL   J. Mol. Biol. 396:646-662(2010).
CC   -!- FUNCTION: Global transcriptional regulator that regulates virulence
CC       factors production by activating or repressing the expression of a
CC       large set of genes in diffusible signal factor (DSF) pathway. It
CC       includes, among others, genes involved in extracellular polysaccharide
CC       (EPS) synthesis, flagellum synthesis, protein and fatty acid
CC       metabolism, multidrug resistance, iron uptake or genes encoding
CC       extracellular enzymes, membrane components and a few transcription
CC       factors. Regulation can be direct or indirect, via regulation of other
CC       transcriptional regulators. Not involved in DSF-mediated biofilm
CC       dispersal. {ECO:0000269|PubMed:17378922}.
CC   -!- ACTIVITY REGULATION: Allosterically inhibited by cyclic di-GMP (c-di-
CC       GMP), which binds to Clp and abolishes its ability to bind its target
CC       gene promoter. {ECO:0000269|PubMed:20004667,
CC       ECO:0000269|PubMed:20008070}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:20004667}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC   -!- INDUCTION: Expression is induced by DSF signal, via the RpfC/RpfG two-
CC       component system. {ECO:0000269|PubMed:17378922}.
CC   -!- DOMAIN: Binding of c-di-GMP appears to trigger the active Clp
CC       conformation into an open form or inactive state, hence abolishing its
CC       DNA-binding ability. {ECO:0000269|PubMed:20004667}.
CC   -!- DISRUPTION PHENOTYPE: Mutant produces less EPS and shows decrease in
CC       cellulase and protease activities. {ECO:0000269|PubMed:17378922}.
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DR   EMBL; M58745; AAA27597.1; -; Genomic_DNA.
DR   EMBL; M92289; AAA27598.1; -; Genomic_DNA.
DR   EMBL; AF111840; AAD20599.1; -; Genomic_DNA.
DR   EMBL; AE008922; AAM39790.1; -; Genomic_DNA.
DR   PIR; A42949; A42949.
DR   RefSeq; NP_635866.1; NC_003902.1.
DR   RefSeq; WP_011035725.1; NC_003902.1.
DR   PDB; 3IWZ; X-ray; 2.30 A; A/B/C/D=1-230.
DR   PDBsum; 3IWZ; -.
DR   AlphaFoldDB; P22260; -.
DR   SMR; P22260; -.
DR   STRING; 190485.XCC0472; -.
DR   EnsemblBacteria; AAM39790; AAM39790; XCC0472.
DR   GeneID; 58011784; -.
DR   KEGG; xcc:XCC0472; -.
DR   PATRIC; fig|190485.4.peg.519; -.
DR   eggNOG; COG0664; Bacteria.
DR   HOGENOM; CLU_075053_3_5_6; -.
DR   OrthoDB; 61906at2; -.
DR   EvolutionaryTrace; P22260; -.
DR   PHI-base; PHI:12171; -.
DR   Proteomes; UP000001010; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0003824; F:catalytic activity; IEA:UniProtKB-KW.
DR   GO; GO:0035438; F:cyclic-di-GMP binding; IDA:UniProtKB.
DR   GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
DR   GO; GO:0003700; F:DNA-binding transcription factor activity; IMP:UniProtKB.
DR   GO; GO:0046983; F:protein dimerization activity; IDA:UniProtKB.
DR   GO; GO:0008152; P:metabolic process; IEA:UniProtKB-KW.
DR   GO; GO:0006355; P:regulation of DNA-templated transcription; IMP:UniProtKB.
DR   CDD; cd00038; CAP_ED; 1.
DR   Gene3D; 2.60.120.10; Jelly Rolls; 1.
DR   Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 1.
DR   InterPro; IPR000595; cNMP-bd_dom.
DR   InterPro; IPR018490; cNMP-bd_dom_sf.
DR   InterPro; IPR012318; HTH_CRP.
DR   InterPro; IPR014710; RmlC-like_jellyroll.
DR   InterPro; IPR018335; Tscrpt_reg_HTH_Crp-type_CS.
DR   InterPro; IPR036388; WH-like_DNA-bd_sf.
DR   InterPro; IPR036390; WH_DNA-bd_sf.
DR   PANTHER; PTHR24567:SF79; CAMP-ACTIVATED GLOBAL TRANSCRIPTIONAL REGULATOR CRP; 1.
DR   PANTHER; PTHR24567; CRP FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN; 1.
DR   Pfam; PF00027; cNMP_binding; 1.
DR   Pfam; PF00325; Crp; 1.
DR   PRINTS; PR00034; HTHCRP.
DR   SMART; SM00100; cNMP; 1.
DR   SMART; SM00419; HTH_CRP; 1.
DR   SUPFAM; SSF51206; cAMP-binding domain-like; 1.
DR   SUPFAM; SSF46785; Winged helix' DNA-binding domain; 1.
DR   PROSITE; PS50042; CNMP_BINDING_3; 1.
DR   PROSITE; PS00042; HTH_CRP_1; 1.
DR   PROSITE; PS51063; HTH_CRP_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Activator; Allosteric enzyme; c-di-GMP; Cytoplasm;
KW   DNA-binding; Reference proteome; Repressor; Transcription;
KW   Transcription regulation; Virulence.
FT   CHAIN           1..230
FT                   /note="CRP-like protein Clp"
FT                   /id="PRO_0000100152"
FT   DOMAIN          158..230
FT                   /note="HTH crp-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00387"
FT   DNA_BIND        190..209
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00387"
FT   BINDING         18..139
FT                   /ligand="a nucleoside 3',5'-cyclic phosphate"
FT                   /ligand_id="ChEBI:CHEBI:58464"
FT   MUTAGEN         70
FT                   /note="D->A: Almost no change in DNA-binding, but decrease
FT                   in c-di-GMP-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         99
FT                   /note="E->A: Decrease in DNA-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         150
FT                   /note="R->A: Decrease in DNA-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         154
FT                   /note="R->A: Almost no change in DNA-binding, but decrease
FT                   in c-di-GMP-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         162
FT                   /note="D->A: Decrease in DNA-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         165
FT                   /note="V->A: Decrease in DNA-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         166
FT                   /note="R->A: Almost no change in DNA-binding, but decrease
FT                   in c-di-GMP-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         170
FT                   /note="D->A: Almost no change in DNA-binding, but decrease
FT                   in c-di-GMP-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   MUTAGEN         195
FT                   /note="R->A: Decrease in DNA-binding."
FT                   /evidence="ECO:0000269|PubMed:20004667"
FT   CONFLICT        98
FT                   /note="R -> H (in Ref. 1; AAA27597 and 2; AAA27598)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        139
FT                   /note="V -> A (in Ref. 3; AAD20599)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        200..202
FT                   /note="SRE -> CAQ (in Ref. 1; AAA27597)"
FT                   /evidence="ECO:0000305"
FT   HELIX           24..31
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          34..39
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          44..46
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          54..61
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          63..68
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          74..80
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          85..87
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   HELIX           89..91
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          100..106
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          108..114
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   HELIX           115..123
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   TURN            124..126
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   HELIX           127..129
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   HELIX           130..157
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   HELIX           160..171
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          178..180
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          183..187
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   HELIX           190..197
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   HELIX           201..213
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          216..220
FT                   /evidence="ECO:0007829|PDB:3IWZ"
FT   STRAND          223..227
FT                   /evidence="ECO:0007829|PDB:3IWZ"
SQ   SEQUENCE   230 AA;  25711 MW;  F9252D2A1D2C1F0B CRC64;
     MSLGNTTVVT TTVRNATPSL TLDAGTIERF LAHSHRRRYP TRTDVFRPGD PAGTLYYVIS
     GSVSIIAEED DDRELVLGYF GSGEFVGEMG LFIESDTREV ILRTRTQCEL AEISYERLQQ
     LFQTSLSPDA PRILYAIGVQ LSKRLLDTTR KASRLAFLDV TDRIVRTLHD LSKEPEAMSH
     PQGTQLRVSR QELARLVGCS REMAGRVLKK LQADGLLHAR GKTVVLYGTR
//