Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Toxin CcdB

Gene

ccdB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Toxic component of a toxin-antitoxin (TA) module, functioning in plasmid maintainence. Responsible for the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Half-life of over 2 hours. Cell killing by CcdB is accompanied by filamentation, defects in chromosome and plasmid segregation, defects in cell division, formation of anucleate cells, decreased DNA synthesis and plasmid loss. Interferes with the activity of DNA gyrase, inducing it to form a covalent GyrA-DNA complex that cannot be resolved, thus promoting breakage of plasmid and chromosomal DNA. DNA breakage requires hydrolyzable ATP. Toxicity is inhibited by labile antitoxin CcdA, which blocks the activity of CcdB; CcdA also removes bound CcdB protein from the CcdB-GyrA complex by forming a CcdA-CcdB complex, a process termed rejuvenation. Also acts to inhibit partitioning of the chromosomal DNA. Functions as a transcriptional corepressor for the ccdAB operon, repression also requires CcdA.6 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor, Toxin

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Toxin CcdB
Alternative name(s):
Cytotoxic protein CcdB
LynB
Protein G
Protein LetD
Gene namesi
Name:ccdB
Synonyms:G, letB, letD
Ordered Locus Names:ECOK12F043
Encoded oniPlasmid F0 Publication
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Pathology & Biotechi

Disruption phenotypei

Disruption of both ccdA and ccdB has no phenotype, except for increased plasmid loss.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi21 – 211Q → L, S or Y: No phenotype. 1 Publication
Mutagenesisi61 – 611W → L, Q, S or Y: No phenotype. 1 Publication
Mutagenesisi99 – 1013Missing : Loss of toxicity, no decrease in protein stability. Still represses ccdAB operon, still forms complex with CcdA.
Mutagenesisi99 – 991W → L, Q, S or Y: Loss of toxicity. 1 Publication
Mutagenesisi100 – 1001G → E or R: Loss of toxicity, no decrease in protein stability. Still represses ccdAB operon, still forms complex with CcdA. 1 Publication
Mutagenesisi101 – 1011I → R: Loss of toxicity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 101101Toxin CcdBPRO_0000068386Add
BLAST

Proteomic databases

PRIDEiP62554.

Interactioni

Subunit structurei

Homodimer. Forms a complex with GyrA, probably a tetramer GyrA2CcdB2, in which GyrA is inactive. Forms a complex with antitoxin CcdA; there are both high- and low-affinity binding sites for CcdA such that both CcdA-CcdB2 and CcdA2CcdB2 complexes can form. The CcdA-CcdB2 trimer is sufficient for rejuvenation, whereas maximal operon repression occurs with CcdA2CcdB2. When the CcdA:CcdB ratio is lower than 1, a CcdA(2)-CcdB4 complex is formed which is devoid of repression activity. In this case repression is alleviated and both proteins are produced.6 Publications

Structurei

Secondary structure

1
101
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 107Combined sources
Beta strandi15 – 195Combined sources
Beta strandi30 – 4213Combined sources
Beta strandi44 – 463Combined sources
Turni48 – 503Combined sources
Beta strandi53 – 564Combined sources
Beta strandi59 – 635Combined sources
Helixi65 – 673Combined sources
Beta strandi69 – 724Combined sources
Helixi73 – 753Combined sources
Beta strandi76 – 827Combined sources
Helixi84 – 863Combined sources
Helixi87 – 9913Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VUBX-ray2.60A/B/C/D1-101[»]
1X75X-ray2.80C/D1-101[»]
2VUBX-ray2.45A/B/C/D/E/F/G/H1-101[»]
3G7ZX-ray2.35A/B1-101[»]
3HPWX-ray1.45A/B1-101[»]
3VUBX-ray1.40A1-101[»]
4VUBX-ray1.45A1-101[»]
ProteinModelPortaliP62554.
SMRiP62554. Positions 1-101.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62554.

Family & Domainsi

Sequence similaritiesi

Belongs to the CcdB toxin family.Curated

Phylogenomic databases

KOiK19163.
OMAiRLMTTDM.

Family and domain databases

Gene3Di2.30.30.110. 1 hit.
InterProiIPR002712. CcdB.
IPR011067. Plasmid_toxin/cell-grow_inhib.
[Graphical view]
PfamiPF01845. CcdB. 1 hit.
[Graphical view]
ProDomiPD012578. PD012578. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF50118. SSF50118. 1 hit.

Sequencei

Sequence statusi: Complete.

P62554-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQFKVYTYKR ESRYRLFVDV QSDIIDTPGR RMVIPLASAR LLSDKVSREL
60 70 80 90 100
YPVVHIGDES WRMMTTDMAS VPVSVIGEEV ADLSHRENDI KNAINLMFWG

I
Length:101
Mass (Da):11,707
Last modified:July 19, 2004 - v1
Checksum:i566AF6681DFE94FE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00594 Genomic DNA. Translation: CAA25244.1.
M12987 Genomic DNA. Translation: AAA24899.1.
AP001918 Genomic DNA. Translation: BAA97913.1.
PIRiT00238.
RefSeqiNP_061422.1. NC_002483.1.
WP_001159868.1. NZ_CP014273.1.
YP_003108267.1. NC_013122.1.

Genome annotation databases

GeneIDi1263593.
8319210.
KEGGipg:1263593.
pg:8319210.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00594 Genomic DNA. Translation: CAA25244.1.
M12987 Genomic DNA. Translation: AAA24899.1.
AP001918 Genomic DNA. Translation: BAA97913.1.
PIRiT00238.
RefSeqiNP_061422.1. NC_002483.1.
WP_001159868.1. NZ_CP014273.1.
YP_003108267.1. NC_013122.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VUBX-ray2.60A/B/C/D1-101[»]
1X75X-ray2.80C/D1-101[»]
2VUBX-ray2.45A/B/C/D/E/F/G/H1-101[»]
3G7ZX-ray2.35A/B1-101[»]
3HPWX-ray1.45A/B1-101[»]
3VUBX-ray1.40A1-101[»]
4VUBX-ray1.45A1-101[»]
ProteinModelPortaliP62554.
SMRiP62554. Positions 1-101.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP62554.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1263593.
8319210.
KEGGipg:1263593.
pg:8319210.

Phylogenomic databases

KOiK19163.
OMAiRLMTTDM.

Miscellaneous databases

EvolutionaryTraceiP62554.
PROiP62554.

Family and domain databases

Gene3Di2.30.30.110. 1 hit.
InterProiIPR002712. CcdB.
IPR011067. Plasmid_toxin/cell-grow_inhib.
[Graphical view]
PfamiPF01845. CcdB. 1 hit.
[Graphical view]
ProDomiPD012578. PD012578. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF50118. SSF50118. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Control of cell division by sex factor F in Escherichia coli. I. The 42.84-43.6 F segment couples cell division of the host bacteria with replication of plasmid DNA."
    Miki T., Yoshioka K., Horiuchi T.
    J. Mol. Biol. 174:605-625(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ROLE IN CELL DEATH.
  2. "F plasmid DNA complete mini-F region (F coordinates 40.301F to 49.869F)."
    Eichenlaub R.
    Submitted (AUG-1986) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Complete nucleotide sequence of the F plasmid: its implications for organization and diversification of plasmid genomes."
    Shimizu H., Saitoh Y., Suda Y., Uehara K., Sampei G., Mizobuchi K.
    Submitted (APR-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / CR63.
  4. "Control of the ccd operon in plasmid F."
    Tam J.E., Kline B.C.
    J. Bacteriol. 171:2353-2360(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-15, FUNCTION IN TRANSCRIPTIONAL REGULATION, DNA-BINDING, SUBUNIT.
  5. "Ham22, a mini-F mutation which is lethal to host cell and promotes recA-dependent induction of lambdoid prophage."
    Karoui H., Bex F., Dreze P., Couturier M.
    EMBO J. 2:1863-1868(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  6. "Mini-F plasmid genes that couple host cell division to plasmid proliferation."
    Ogura T., Hiraga S.
    Proc. Natl. Acad. Sci. U.S.A. 80:4784-4788(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: ROLE IN PLASMID MAINTENANCE, DISRUPTION PHENOTYPE.
  7. "The F plasmid ccd autorepressor is a complex of CcdA and CcdB proteins."
    Tam J.E., Kline B.C.
    Mol. Gen. Genet. 219:26-32(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN TRANSCRIPTIONAL REGULATION, DNA-BINDING, SUBUNIT.
  8. "Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes."
    Bernard P., Couturier M.
    J. Mol. Biol. 226:735-745(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TOXIN, FUNCTION IN DNA BREAKAGE, INHIBITION BY CCDA.
  9. "The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase."
    Bernard P., Kezdy K.E., Van Melderen L., Steyaert J., Wyns L., Pato M.L., Higgins P.N., Couturier M.
    J. Mol. Biol. 234:534-541(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION OF REJUVENATION ACTIVITY, ATP REQUIRED FOR DNA BREAKAGE.
  10. "Lon-dependent proteolysis of CcdA is the key control for activation of CcdB in plasmid-free segregant bacteria."
    Van Melderen L., Bernard P., Couturier M.
    Mol. Microbiol. 11:1151-1157(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: HALF-LIFE.
  11. "F plasmid CcdB killer protein: ccdB gene mutants coding for non-cytotoxic proteins which retain their regulatory functions."
    Bahassi E.M., Salmon M.A., Van Melderen L., Bernard P., Couturier M.
    Mol. Microbiol. 15:1031-1037(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLN-21; TRP-61; TRP-99; GLY-100 AND ILE-101.
  12. "Partner switching mechanisms in inactivation and rejuvenation of Escherichia coli DNA gyrase by F plasmid proteins LetD (CcdB) and LetA (CcdA)."
    Maki S., Takiguchi S., Horiuchi T., Sekimizu K., Miki T.
    J. Mol. Biol. 256:473-482(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TOXIN, FUNCTION IN DNA BREAKAGE, REJUVENATION, SUBUNIT.
  13. "The ratio between CcdA and CcdB modulates the transcriptional repression of the ccd poison-antidote system."
    Afif H., Allali N., Couturier M., Van Melderen L.
    Mol. Microbiol. 41:73-82(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: MODE OF TRANSCRIPTIONAL REGULATION.
  14. Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS), SUBUNIT.
  15. "Molecular basis of gyrase poisoning by the addiction toxin CcdB."
    Dao-Thi M.H., Van Melderen L., De Genst E., Afif H., Buts L., Wyns L., Loris R.
    J. Mol. Biol. 348:1091-1102(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH GYRA.
  16. "Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain."
    De Jonge N., Garcia-Pino A., Buts L., Haesaerts S., Charlier D., Zangger K., Wyns L., De Greve H., Loris R.
    Mol. Cell 35:154-163(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiCCDB_ECOLI
AccessioniPrimary (citable) accession number: P62554
Secondary accession number(s): P05703
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2004
Last sequence update: July 19, 2004
Last modified: May 11, 2016
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Plasmid

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.