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Protein

tRNA(fMet)-specific endonuclease VapC

Gene

vapC

Organism
Shigella flexneri
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Toxic component of a type II toxin-antitoxin (TA) system. 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

Keywordsi

Molecular functionEndonuclease, Hydrolase, Nuclease
Biological processToxin-antitoxin system
LigandMagnesium, 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

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

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

Phylogenomic databases

eggNOGiENOG4105M0J Bacteria
COG1487 LUCA
HOGENOMiHOG000121274
KOiK18828
OMAiNTAEFTR

Family and domain databases

HAMAPiMF_00265 VapC_Nob1, 1 hit
InterProiView protein in InterPro
IPR029060 PIN-like_dom_sf
IPR002716 PIN_dom
IPR022907 VapC_family
PfamiView protein in Pfam
PF01850 PIN, 1 hit
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_MTPK01000145.1
YP_009062544.1, NC_024996.1

Genome annotation databases

EnsemblBacteriaiAAL72335; AAL72335; SF_p0245
GeneIDi1238038
876621
KEGGisfl:CP0245
PATRICifig|198214.7.peg.5506

Similar proteinsi

Entry informationi

Entry nameiVAPC_SHIFL
AccessioniPrimary (citable) accession number: O06662
Secondary accession number(s): Q7BCI3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 28, 2011
Last sequence update: July 1, 1997
Last modified: April 25, 2018
This is version 104 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Plasmid, Reference proteome
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Main funding by: National Institutes of Health