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
//
