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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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia

Pathology & Biotechi

Disruption phenotypei

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

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi21Q → L, S or Y: No phenotype. 1 Publication1
Mutagenesisi61W → L, Q, S or Y: No phenotype. 1 Publication1
Mutagenesisi99 – 101Missing : Loss of toxicity, no decrease in protein stability. Still represses ccdAB operon, still forms complex with CcdA. 3
Mutagenesisi99W → L, Q, S or Y: Loss of toxicity. 1 Publication1
Mutagenesisi100G → E or R: Loss of toxicity, no decrease in protein stability. Still represses ccdAB operon, still forms complex with CcdA. 1 Publication1
Mutagenesisi101I → R: Loss of toxicity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000683861 – 101Toxin CcdBAdd BLAST101

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

1101
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 10Combined sources7
Beta strandi15 – 19Combined sources5
Beta strandi30 – 42Combined sources13
Beta strandi44 – 46Combined sources3
Turni48 – 50Combined sources3
Beta strandi53 – 56Combined sources4
Beta strandi59 – 63Combined sources5
Helixi65 – 67Combined sources3
Beta strandi69 – 72Combined sources4
Helixi73 – 75Combined sources3
Beta strandi76 – 82Combined sources7
Helixi84 – 86Combined sources3
Helixi87 – 99Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62554.

Family & Domainsi

Sequence similaritiesi

Belongs to the CcdB toxin family.Curated

Phylogenomic databases

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.

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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi1263593.
8319210.

Phylogenomic databases

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...

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: November 30, 2016
This is version 79 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.