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P22260

- CLP_XANCP

UniProt

P22260 - CLP_XANCP

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Protein

CRP-like protein Clp

Gene

clp

Organism
Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Global transcriptional regulator that regulates virulence factors production by activating or repressing the expression of a large set of genes in diffusible signal factor (DSF) pathway. It includes, among others, genes involved in extracellular polysaccharide (EPS) synthesis, flagellum synthesis, protein and fatty acid metabolism, multidrug resistance, iron uptake or genes encoding extracellular enzymes, membrane components and a few transcription factors. Regulation can be direct or indirect, via regulation of other transcriptional regulators. Not involved in DSF-mediated biofilm dispersal.1 Publication

Enzyme regulationi

Allosterically inhibited by cyclic di-GMP (c-di-GMP), which binds to Clp and abolishes its ability to bind its target gene promoter.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi18 – 139122cNMPAdd
BLAST
DNA bindingi190 – 20920H-T-H motifPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. catalytic activity Source: UniProtKB-KW
  2. cyclic-di-GMP binding Source: UniProtKB
  3. DNA binding Source: UniProtKB
  4. protein dimerization activity Source: UniProtKB
  5. sequence-specific DNA binding transcription factor activity Source: UniProtKB

GO - Biological processi

  1. pathogenesis Source: UniProtKB-KW
  2. regulation of transcription, DNA-templated Source: UniProtKB
  3. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation, Virulence

Keywords - Ligandi

c-di-GMP, DNA-binding

Enzyme and pathway databases

BioCyciXCAM190485:GIXZ-472-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
CRP-like protein Clp
Alternative name(s):
Catabolite activation-like protein
Short name:
CAP-like
Gene namesi
Name:clp
Ordered Locus Names:XCC0472
OrganismiXanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)
Taxonomic identifieri190485 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
ProteomesiUP000001010: Chromosome

Subcellular locationi

Cytoplasm Curated

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Mutant produces less EPS and shows decrease in cellulase and protease activities.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi70 – 701D → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication
Mutagenesisi99 – 991E → A: Decrease in DNA-binding. 1 Publication
Mutagenesisi150 – 1501R → A: Decrease in DNA-binding. 1 Publication
Mutagenesisi154 – 1541R → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication
Mutagenesisi162 – 1621D → A: Decrease in DNA-binding. 1 Publication
Mutagenesisi165 – 1651V → A: Decrease in DNA-binding. 1 Publication
Mutagenesisi166 – 1661R → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication
Mutagenesisi170 – 1701D → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication
Mutagenesisi195 – 1951R → A: Decrease in DNA-binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 230230CRP-like protein ClpPRO_0000100152Add
BLAST

Expressioni

Inductioni

Expression is induced by DSF signal, via the RpfC/RpfG two-component system.1 Publication

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi190485.XCC0472.

Structurei

Secondary structure

1
230
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi24 – 318Combined sources
Beta strandi34 – 396Combined sources
Beta strandi44 – 463Combined sources
Beta strandi54 – 618Combined sources
Beta strandi63 – 686Combined sources
Beta strandi74 – 807Combined sources
Beta strandi85 – 873Combined sources
Helixi89 – 913Combined sources
Beta strandi100 – 1067Combined sources
Beta strandi108 – 1147Combined sources
Helixi115 – 1239Combined sources
Turni124 – 1263Combined sources
Helixi127 – 1293Combined sources
Helixi130 – 15728Combined sources
Helixi160 – 17112Combined sources
Beta strandi178 – 1803Combined sources
Beta strandi183 – 1875Combined sources
Helixi190 – 1978Combined sources
Helixi201 – 21313Combined sources
Beta strandi216 – 2205Combined sources
Beta strandi223 – 2275Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3IWZX-ray2.30A/B/C/D1-230[»]
ProteinModelPortaliP22260.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22260.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini158 – 23073HTH crp-typePROSITE-ProRule annotationAdd
BLAST

Domaini

Binding of c-di-GMP appears to trigger the active Clp conformation into an open form or inactive state, hence abolishing its DNA-binding ability.1 Publication

Sequence similaritiesi

Contains 1 cyclic nucleotide-binding domain.PROSITE-ProRule annotation
Contains 1 HTH crp-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0664.
HOGENOMiHOG000250565.
KOiK10914.
OMAiIMAEEDD.
OrthoDBiEOG69GZGV.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
2.60.120.10. 1 hit.
InterProiIPR018490. cNMP-bd-like.
IPR000595. cNMP-bd_dom.
IPR012318. HTH_CRP_2.
IPR014710. RmlC-like_jellyroll.
IPR001808. Tscrpt_reg_HTH_Crp.
IPR018335. Tscrpt_reg_HTH_Crp-type_CS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00027. cNMP_binding. 1 hit.
PF00325. Crp. 1 hit.
[Graphical view]
PRINTSiPR00034. HTHCRP.
SMARTiSM00100. cNMP. 1 hit.
SM00419. HTH_CRP. 1 hit.
[Graphical view]
SUPFAMiSSF51206. SSF51206. 1 hit.
PROSITEiPS50042. CNMP_BINDING_3. 1 hit.
PS00042. HTH_CRP_1. 1 hit.
PS51063. HTH_CRP_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P22260-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSLGNTTVVT TTVRNATPSL TLDAGTIERF LAHSHRRRYP TRTDVFRPGD
60 70 80 90 100
PAGTLYYVIS GSVSIIAEED DDRELVLGYF GSGEFVGEMG LFIESDTREV
110 120 130 140 150
ILRTRTQCEL AEISYERLQQ LFQTSLSPDA PRILYAIGVQ LSKRLLDTTR
160 170 180 190 200
KASRLAFLDV TDRIVRTLHD LSKEPEAMSH PQGTQLRVSR QELARLVGCS
210 220 230
REMAGRVLKK LQADGLLHAR GKTVVLYGTR
Length:230
Mass (Da):25,711
Last modified:July 11, 2002 - v2
Checksum:iF9252D2A1D2C1F0B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti98 – 981R → H in AAA27597. (PubMed:2170330)Curated
Sequence conflicti98 – 981R → H in AAA27598. (PubMed:1322886)Curated
Sequence conflicti139 – 1391V → A in AAD20599. (PubMed:11361081)Curated
Sequence conflicti200 – 2023SRE → CAQ in AAA27597. (PubMed:2170330)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58745 Genomic DNA. Translation: AAA27597.1.
M92289 Genomic DNA. Translation: AAA27598.1.
AF111840 Genomic DNA. Translation: AAD20599.1.
AE008922 Genomic DNA. Translation: AAM39790.1.
PIRiA42949.
RefSeqiNP_635866.1. NC_003902.1.

Genome annotation databases

EnsemblBacteriaiAAM39790; AAM39790; XCC0472.
GeneIDi1000958.
KEGGixcc:XCC0472.
PATRICi24071563. VBIXanCam115730_0519.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58745 Genomic DNA. Translation: AAA27597.1 .
M92289 Genomic DNA. Translation: AAA27598.1 .
AF111840 Genomic DNA. Translation: AAD20599.1 .
AE008922 Genomic DNA. Translation: AAM39790.1 .
PIRi A42949.
RefSeqi NP_635866.1. NC_003902.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
3IWZ X-ray 2.30 A/B/C/D 1-230 [» ]
ProteinModelPortali P22260.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 190485.XCC0472.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAM39790 ; AAM39790 ; XCC0472 .
GeneIDi 1000958.
KEGGi xcc:XCC0472.
PATRICi 24071563. VBIXanCam115730_0519.

Phylogenomic databases

eggNOGi COG0664.
HOGENOMi HOG000250565.
KOi K10914.
OMAi IMAEEDD.
OrthoDBi EOG69GZGV.

Enzyme and pathway databases

BioCyci XCAM190485:GIXZ-472-MONOMER.

Miscellaneous databases

EvolutionaryTracei P22260.

Family and domain databases

Gene3Di 1.10.10.10. 1 hit.
2.60.120.10. 1 hit.
InterProi IPR018490. cNMP-bd-like.
IPR000595. cNMP-bd_dom.
IPR012318. HTH_CRP_2.
IPR014710. RmlC-like_jellyroll.
IPR001808. Tscrpt_reg_HTH_Crp.
IPR018335. Tscrpt_reg_HTH_Crp-type_CS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
Pfami PF00027. cNMP_binding. 1 hit.
PF00325. Crp. 1 hit.
[Graphical view ]
PRINTSi PR00034. HTHCRP.
SMARTi SM00100. cNMP. 1 hit.
SM00419. HTH_CRP. 1 hit.
[Graphical view ]
SUPFAMi SSF51206. SSF51206. 1 hit.
PROSITEi PS50042. CNMP_BINDING_3. 1 hit.
PS00042. HTH_CRP_1. 1 hit.
PS51063. HTH_CRP_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity."
    de Crecy-Lagard V., Glaser P., Lejeune P., Sismeiro O., Barber C.E., Daniels M.J., Danchin A.
    J. Bacteriol. 172:5877-5883(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 13951 / NCIB 11803 / NRRL B-1459.
  2. "DNA binding specificity and sequence of Xanthomonas campestris catabolite gene activator protein-like protein."
    Dong Q., Ebright R.H.
    J. Bacteriol. 174:5457-5461(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "The early stages of filamentous phage phiLf infection require the host transcription factor, Clp."
    Lee T.C., Chen S.T., Lee M.C., Chang C.M., Chen C.H., Weng S.F., Tseng Y.H.
    J. Mol. Microbiol. Biotechnol. 3:471-481(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Xc17.
  4. "Comparison of the genomes of two Xanthomonas pathogens with differing host specificities."
    da Silva A.C.R., Ferro J.A., Reinach F.C., Farah C.S., Furlan L.R., Quaggio R.B., Monteiro-Vitorello C.B., Van Sluys M.A., Almeida N.F. Jr., Alves L.M.C., do Amaral A.M., Bertolini M.C., Camargo L.E.A., Camarotte G., Cannavan F., Cardozo J., Chambergo F., Ciapina L.P.
    , Cicarelli R.M.B., Coutinho L.L., Cursino-Santos J.R., El-Dorry H., Faria J.B., Ferreira A.J.S., Ferreira R.C.C., Ferro M.I.T., Formighieri E.F., Franco M.C., Greggio C.C., Gruber A., Katsuyama A.M., Kishi L.T., Leite R.P., Lemos E.G.M., Lemos M.V.F., Locali E.C., Machado M.A., Madeira A.M.B.N., Martinez-Rossi N.M., Martins E.C., Meidanis J., Menck C.F.M., Miyaki C.Y., Moon D.H., Moreira L.M., Novo M.T.M., Okura V.K., Oliveira M.C., Oliveira V.R., Pereira H.A., Rossi A., Sena J.A.D., Silva C., de Souza R.F., Spinola L.A.F., Takita M.A., Tamura R.E., Teixeira E.C., Tezza R.I.D., Trindade dos Santos M., Truffi D., Tsai S.M., White F.F., Setubal J.C., Kitajima J.P.
    Nature 417:459-463(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 33913 / NCPPB 528 / LMG 568.
  5. "Xanthomonas campestris cell-cell communication involves a putative nucleotide receptor protein Clp and a hierarchical signalling network."
    He Y.W., Ng A.Y., Xu M., Lin K., Wang L.H., Dong Y.H., Zhang L.H.
    Mol. Microbiol. 64:281-292(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION, DISRUPTION PHENOTYPE.
    Strain: Xc1.
  6. "The cyclic nucleotide monophosphate domain of Xanthomonas campestris global regulator Clp defines a new class of cyclic di-GMP effectors."
    Tao F., He Y.W., Wu D.H., Swarup S., Zhang L.H.
    J. Bacteriol. 192:1020-1029(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: DNA-BINDING, ENZYME REGULATION.
    Strain: 8004.
  7. "The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris."
    Chin K.H., Lee Y.C., Tu Z.L., Chen C.H., Tseng Y.H., Yang J.M., Ryan R.P., McCarthy Y., Dow J.M., Wang A.H., Chou S.H.
    J. Mol. Biol. 396:646-662(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), DNA-BINDING, ENZYME REGULATION, SUBUNIT, DOMAIN, MUTAGENESIS OF ASP-70; GLU-99; ARG-150; ARG-154; ASP-162; VAL-165; ARG-166; ASP-170 AND ARG-195.
    Strain: Xc17.

Entry informationi

Entry nameiCLP_XANCP
AccessioniPrimary (citable) accession number: P22260
Secondary accession number(s): Q9S6B5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: July 11, 2002
Last modified: November 26, 2014
This is version 107 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3