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Protein

CRP-like protein Clp

Gene

clp

Organism
Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Nucleotide bindingi18 – 139cNMPAdd BLAST122
DNA bindingi190 – 209H-T-H motifPROSITE-ProRule annotationAdd BLAST20

GO - Molecular functioni

  • catalytic activity Source: UniProtKB-KW
  • cyclic-di-GMP binding Source: UniProtKB
  • DNA binding Source: UniProtKB
  • protein dimerization activity Source: UniProtKB
  • transcription factor activity, sequence-specific DNA binding Source: UniProtKB

GO - Biological processi

  • pathogenesis Source: UniProtKB-KW
  • regulation of transcription, DNA-templated Source: UniProtKB
  • 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

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 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)
Taxonomic identifieri190485 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
Proteomesi
  • UP000001010 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Mutagenesisi70D → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication1
Mutagenesisi99E → A: Decrease in DNA-binding. 1 Publication1
Mutagenesisi150R → A: Decrease in DNA-binding. 1 Publication1
Mutagenesisi154R → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication1
Mutagenesisi162D → A: Decrease in DNA-binding. 1 Publication1
Mutagenesisi165V → A: Decrease in DNA-binding. 1 Publication1
Mutagenesisi166R → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication1
Mutagenesisi170D → A: Almost no change in DNA-binding, but decrease in c-di-GMP-binding. 1 Publication1
Mutagenesisi195R → A: Decrease in DNA-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001001521 – 230CRP-like protein ClpAdd BLAST230

Expressioni

Inductioni

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

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • protein dimerization activity Source: UniProtKB

Protein-protein interaction databases

STRINGi190485.XCC0472.

Structurei

Secondary structure

1230
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi24 – 31Combined sources8
Beta strandi34 – 39Combined sources6
Beta strandi44 – 46Combined sources3
Beta strandi54 – 61Combined sources8
Beta strandi63 – 68Combined sources6
Beta strandi74 – 80Combined sources7
Beta strandi85 – 87Combined sources3
Helixi89 – 91Combined sources3
Beta strandi100 – 106Combined sources7
Beta strandi108 – 114Combined sources7
Helixi115 – 123Combined sources9
Turni124 – 126Combined sources3
Helixi127 – 129Combined sources3
Helixi130 – 157Combined sources28
Helixi160 – 171Combined sources12
Beta strandi178 – 180Combined sources3
Beta strandi183 – 187Combined sources5
Helixi190 – 197Combined sources8
Helixi201 – 213Combined sources13
Beta strandi216 – 220Combined sources5
Beta strandi223 – 227Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IWZX-ray2.30A/B/C/D1-230[»]
ProteinModelPortaliP22260.
SMRiP22260.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22260.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini158 – 230HTH crp-typePROSITE-ProRule annotationAdd BLAST73

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

eggNOGiENOG4107RYR. Bacteria.
COG0664. LUCA.
HOGENOMiHOG000250565.
KOiK10914.
OMAiCAHEICR.

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.
IPR014710. RmlC-like_jellyroll.
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]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF51206. 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)DescriptionActionsGraphical viewLength
Sequence conflicti98R → H in AAA27597 (PubMed:2170330).Curated1
Sequence conflicti98R → H in AAA27598 (PubMed:1322886).Curated1
Sequence conflicti139V → A in AAD20599 (PubMed:11361081).Curated1
Sequence conflicti200 – 202SRE → CAQ in AAA27597 (PubMed:2170330).Curated3

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.
WP_011035725.1. 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.
PIRiA42949.
RefSeqiNP_635866.1. NC_003902.1.
WP_011035725.1. NC_003902.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IWZX-ray2.30A/B/C/D1-230[»]
ProteinModelPortaliP22260.
SMRiP22260.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi190485.XCC0472.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiENOG4107RYR. Bacteria.
COG0664. LUCA.
HOGENOMiHOG000250565.
KOiK10914.
OMAiCAHEICR.

Miscellaneous databases

EvolutionaryTraceiP22260.

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.
IPR014710. RmlC-like_jellyroll.
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]
SUPFAMiSSF46785. SSF46785. 1 hit.
SSF51206. SSF51206. 1 hit.
PROSITEiPS50042. CNMP_BINDING_3. 1 hit.
PS00042. HTH_CRP_1. 1 hit.
PS51063. HTH_CRP_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

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 2, 2016
This is version 119 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.