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Protein

tRNA(fMet)-specific endonuclease VapC

Gene

vapC

Organism
Shigella flexneri
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Toxic component of a toxin-antitoxin (TA) module. A tRNA-(fMet) endonuclease, it cleaves both charged and uncharged tRNA-(fMet) between positions 38 and 39 at the anticodon stem-loop boundary. Does not cleave tRNA(Met), tRNA(Arg2), tRNA(His), tRNA(Leu), tRNA(Phe) tRNA(Thr1), tRNA(Tyr) or tRNA(Val). Overexpression in E.coli inhibits translation, leads to loss of cell growth and degradation of tRNA(fMet); these effects are neutralized by expression of cognate antitoxin VapB. The VapB/VapC complex probably regulates transcription of its own promoter.
Ectopic overexpression in E.coli induces the YoeB toxin, but this is not the cause of VapC toxicity.

Cofactori

Mg2+Curated

Enzyme regulationi

Inhibited by EDTA.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi7MagnesiumSequence analysis1
Metal bindingi98MagnesiumSequence analysis1

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Toxin

Keywords - Ligandi

Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
tRNA(fMet)-specific endonuclease VapC (EC:3.1.-.-)
Alternative name(s):
RNase VapC
Toxin VapC
Gene namesi
Name:vapC
Synonyms:mvpA, stborf2
Ordered Locus Names:CP0245
Encoded oniPlasmid pCP3011 Publication
Plasmid pMYSH60004 Publications
Plasmid pWR1001 Publication
OrganismiShigella flexneri
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeShigella
Proteomesi
  • UP000001006 Componenti: Plasmid pCP301

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004109811 – 132tRNA(fMet)-specific endonuclease VapCAdd BLAST132

Proteomic databases

PaxDbiO06662.
PRIDEiO06662.

Expressioni

Inductioni

Degradation of tRNA(fMet) is induced by chloramphenicol treatment, suggesting the antitoxin is unstable.1 Publication

Interactioni

Subunit structurei

Forms a hetero-octamer (4 VapB and 4 VapC) complex with antitoxin VapB. The complex binds 2 different sites in the vapBC promoter, probably via VapB dimerization.2 Publications

Protein-protein interaction databases

STRINGi198214.CP0245.

Structurei

Secondary structure

1132
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 6Combined sources3
Helixi8 – 16Combined sources9
Helixi20 – 28Combined sources9
Turni29 – 31Combined sources3
Beta strandi32 – 36Combined sources5
Helixi37 – 49Combined sources13
Helixi53 – 64Combined sources12
Beta strandi67 – 70Combined sources4
Helixi74 – 90Combined sources17
Helixi96 – 107Combined sources12
Beta strandi111 – 113Combined sources3
Helixi117 – 120Combined sources4
Beta strandi128 – 130Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TNDX-ray2.70A/C/E/G1-132[»]
5ECDX-ray1.75A/B2-132[»]
5ECWX-ray1.94A/B2-132[»]
5ECYX-ray2.00A/B/C/D/E/F/G/H2-132[»]
5ED0X-ray2.10A/B/C/D/E/F/G/H/I/J/K/L2-132[»]
ProteinModelPortaliO06662.
SMRiO06662.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO06662.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini5 – 131PINcAdd BLAST127

Sequence similaritiesi

Belongs to the PINc/VapC protein family.Curated
Contains 1 PINc domain.Curated

Phylogenomic databases

eggNOGiENOG4105M0J. Bacteria.
COG1487. LUCA.
HOGENOMiHOG000121274.
KOiK18828.
OMAiIDPRAIC.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00265. VapC_Nob1. 1 hit.
InterProiIPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR022907. VapC_family.
[Graphical view]
PfamiPF01850. PIN. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.

Sequencei

Sequence statusi: Complete.

O06662-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLKFMLDTNI CIFTIKNKPA SVRERFNLNQ GKMCISSVTL MELIYGAEKS
60 70 80 90 100
QMPERNLAVI EGFVSRIDVL DYDAAAATHT GQIRAELARQ GRPVGPFDQM
110 120 130
IAGHARSRGL IIVTNNTREF ERVGGLRTED WS
Length:132
Mass (Da):14,817
Last modified:July 1, 1997 - v1
Checksum:i4C64DB25249C2B70
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82621 Genomic DNA. Translation: AAB58157.1.
AL391753 Genomic DNA. Translation: CAC05862.1.
AF386526 Genomic DNA. Translation: AAL72335.1.
RefSeqiNP_085412.1. NC_002698.1.
NP_858378.1. NC_004851.1.
WP_000911311.1. NZ_LVJC01000140.1.
YP_009062544.1. NC_024996.1.

Genome annotation databases

EnsemblBacteriaiAAL72335; AAL72335; SF_p0245.
GeneIDi1238038.
876621.
KEGGisfl:CP0245.
PATRICi18722830. VBIShiFle86970_5506.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U82621 Genomic DNA. Translation: AAB58157.1.
AL391753 Genomic DNA. Translation: CAC05862.1.
AF386526 Genomic DNA. Translation: AAL72335.1.
RefSeqiNP_085412.1. NC_002698.1.
NP_858378.1. NC_004851.1.
WP_000911311.1. NZ_LVJC01000140.1.
YP_009062544.1. NC_024996.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3TNDX-ray2.70A/C/E/G1-132[»]
5ECDX-ray1.75A/B2-132[»]
5ECWX-ray1.94A/B2-132[»]
5ECYX-ray2.00A/B/C/D/E/F/G/H2-132[»]
5ED0X-ray2.10A/B/C/D/E/F/G/H/I/J/K/L2-132[»]
ProteinModelPortaliO06662.
SMRiO06662.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198214.CP0245.

Proteomic databases

PaxDbiO06662.
PRIDEiO06662.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL72335; AAL72335; SF_p0245.
GeneIDi1238038.
876621.
KEGGisfl:CP0245.
PATRICi18722830. VBIShiFle86970_5506.

Phylogenomic databases

eggNOGiENOG4105M0J. Bacteria.
COG1487. LUCA.
HOGENOMiHOG000121274.
KOiK18828.
OMAiIDPRAIC.

Miscellaneous databases

EvolutionaryTraceiO06662.

Family and domain databases

Gene3Di3.40.50.1010. 1 hit.
HAMAPiMF_00265. VapC_Nob1. 1 hit.
InterProiIPR002716. PIN_dom.
IPR029060. PIN_domain-like.
IPR022907. VapC_family.
[Graphical view]
PfamiPF01850. PIN. 1 hit.
[Graphical view]
SUPFAMiSSF88723. SSF88723. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiVAPC_SHIFL
AccessioniPrimary (citable) accession number: O06662
Secondary accession number(s): Q7BCI3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: July 1, 1997
Last modified: November 30, 2016
This is version 93 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, Complete proteome, 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.