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Protein

Endoribonuclease EndoA

Gene

ndoA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Toxic component of a type II toxin-antitoxin (TA) module. Specific for 5'-UACAU-3' sequences, cleaving after the first U (PubMed:21763692). Yields cleavage products with 3' phosphate and 5' hydroxyl groups (PubMed:15882409). Cannot digest substrate with a UUdUACAUAA cleavage site (PubMed:24120662). Overexpression is toxic for cell growth (shown in E.coli), probably by inhibiting protein synthesis through the cleavage of single-stranded RNA. The toxicity is reversed by the antitoxin EndoAI. Toxin activity cannot be inhibited by MazE from E.coli. The EndoA-EndoAI complex does not seem to bind its own promoter (PubMed:24120662).4 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei25 – 251Transition state stabilizer1 Publication

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease, Toxin

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciBSUB:BSU04660-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Endoribonuclease EndoA1 Publication (EC:3.1.27.-1 Publication)
Alternative name(s):
Toxin EndoA
mRNA interferase EndoA
mRNA interferase MazF-bs1 Publication
Short name:
MazF-bs
Gene namesi
Name:ndoA1 Publication
Synonyms:mazF, ydcE
Ordered Locus Names:BSU04660
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU04660. [Micado]

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi10 – 101F → A: Remains toxic in E.coli. 1 Publication
Mutagenesisi19 – 191S → A: Partially toxic in E.coli. 1 Publication
Mutagenesisi21 – 211Q → A: Not toxic in E.coli. 1 Publication
Mutagenesisi25 – 251R → A: Not toxic in E.coli, 50-fold decreased RNA-binding. 1 Publication
Mutagenesisi32 – 321N → A: Not toxic in E.coli. 1 Publication
Mutagenesisi48 – 481T → A: Not toxic in E.coli. 1 Publication
Mutagenesisi50 – 501Q → A: Remains toxic in E.coli. 1 Publication
Mutagenesisi53 – 531K → A: Not toxic in E.coli, 70-fold decreased RNA-binding. 1 Publication
Mutagenesisi56 – 561L → A: Not toxic in E.coli. 1 Publication
Mutagenesisi59 – 591H → A: Not toxic in E.coli. 1 Publication
Mutagenesisi71 – 711R → A: Remains toxic in E.coli. 1 Publication
Mutagenesisi73 – 731S → A: Not toxic in E.coli, 100-fold decreased RNA-binding. 1 Publication
Mutagenesisi78 – 781E → A: Not toxic in E.coli, 625-fold decreased RNA-binding. 1 Publication
Mutagenesisi79 – 791Q → A: Not toxic in E.coli. 1 Publication
Mutagenesisi90 – 901D → A: Remains toxic in E.coli. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 116116Endoribonuclease EndoAPRO_0000201900Add
BLAST

Proteomic databases

PaxDbiP96622.

Interactioni

Subunit structurei

Homodimer (PubMed:14517982, PubMed:24120662). Forms a complex with antitoxin EndoAI in which the toxin activity is inhibited (PubMed:15882409). One dimer binds a ssRNA substrate, forms a heterohexamer composed of alternating toxin and antitoxin homodimers which inhibits the endoribonuclease activity. Antitoxin prevents RNA binding to the endoribonuclease (PubMed:24120662).3 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100002638.

Structurei

Secondary structure

1
116
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 126Combined sources
Beta strandi23 – 297Combined sources
Helixi33 – 386Combined sources
Beta strandi40 – 5011Combined sources
Beta strandi59 – 624Combined sources
Helixi64 – 674Combined sources
Beta strandi73 – 8412Combined sources
Helixi85 – 873Combined sources
Beta strandi88 – 947Combined sources
Helixi97 – 11014Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NE8X-ray2.10A2-116[»]
4MDXX-ray1.50A/B1-116[»]
4ME7X-ray2.92A/B/C/D2-116[»]
ProteinModelPortaliP96622.
SMRiP96622. Positions 1-116.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP96622.

Family & Domainsi

Sequence similaritiesi

Belongs to the PemK/MazF family.Curated

Phylogenomic databases

eggNOGiCOG2337.
HOGENOMiHOG000290184.
InParanoidiP96622.
KOiK07171.
OMAiNQYSPTT.
OrthoDBiEOG64BQCS.
PhylomeDBiP96622.

Family and domain databases

Gene3Di2.30.30.110. 1 hit.
InterProiIPR003477. PemK-like.
IPR011067. Plasmid_toxin/cell-grow_inhib.
[Graphical view]
PfamiPF02452. PemK. 1 hit.
[Graphical view]
PIRSFiPIRSF033490. MazF. 1 hit.
SUPFAMiSSF50118. SSF50118. 1 hit.

Sequencei

Sequence statusi: Complete.

P96622-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIVKRGDVYF ADLSPVVGSE QGGVRPVLVI QNDIGNRFSP TAIVAAITAQ
60 70 80 90 100
IQKAKLPTHV EIDAKRYGFE RDSVILLEQI RTIDKQRLTD KITHLDDEMM
110
DKVDEALQIS LALIDF
Length:116
Mass (Da):12,978
Last modified:May 1, 1997 - v1
Checksum:iFE89144E62BD2B7C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19303.1.
AL009126 Genomic DNA. Translation: CAB12273.1.
PIRiC69773.
RefSeqiNP_388347.1. NC_000964.3.
WP_003156187.1. NZ_JNCM01000031.1.

Genome annotation databases

EnsemblBacteriaiCAB12273; CAB12273; BSU04660.
GeneIDi939935.
9779343.
KEGGibsu:BSU04660.
PATRICi18972516. VBIBacSub10457_0486.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19303.1.
AL009126 Genomic DNA. Translation: CAB12273.1.
PIRiC69773.
RefSeqiNP_388347.1. NC_000964.3.
WP_003156187.1. NZ_JNCM01000031.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NE8X-ray2.10A2-116[»]
4MDXX-ray1.50A/B1-116[»]
4ME7X-ray2.92A/B/C/D2-116[»]
ProteinModelPortaliP96622.
SMRiP96622. Positions 1-116.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100002638.

Proteomic databases

PaxDbiP96622.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12273; CAB12273; BSU04660.
GeneIDi939935.
9779343.
KEGGibsu:BSU04660.
PATRICi18972516. VBIBacSub10457_0486.

Organism-specific databases

GenoListiBSU04660. [Micado]

Phylogenomic databases

eggNOGiCOG2337.
HOGENOMiHOG000290184.
InParanoidiP96622.
KOiK07171.
OMAiNQYSPTT.
OrthoDBiEOG64BQCS.
PhylomeDBiP96622.

Enzyme and pathway databases

BioCyciBSUB:BSU04660-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP96622.

Family and domain databases

Gene3Di2.30.30.110. 1 hit.
InterProiIPR003477. PemK-like.
IPR011067. Plasmid_toxin/cell-grow_inhib.
[Graphical view]
PfamiPF02452. PemK. 1 hit.
[Graphical view]
PIRSFiPIRSF033490. MazF. 1 hit.
SUPFAMiSSF50118. SSF50118. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A 148 kbp sequence of the region between 35 and 47 degree of the Bacillus subtilis genome."
    Kasahara Y., Nakai S., Lee S., Sadaie Y., Ogasawara N.
    Submitted (MAR-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "The Bacillus subtilis ydcDE operon encodes an endoribonuclease of the MazF/PemK family and its inhibitor."
    Pellegrini O., Mathy N., Gogos A., Shapiro L., Condon C.
    Mol. Microbiol. 56:1139-1148(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN ENDORIBONUCLEASE, CATALYTIC ACTIVITY, INHIBITION BY ENDOAI, SUBUNIT, EXPRESSION IN E.COLI.
    Strain: 168.
  4. "Bacillus subtilis MazF-bs (EndoA) is a UACAU-specific mRNA interferase."
    Park J.H., Yamaguchi Y., Inouye M.
    FEBS Lett. 585:2526-2532(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS AN MRNA INTERFERASE, INHIBITION BY ENDOAI, EXPRESSION IN E.COLI.
    Strain: 168.
  5. "Replacement of all arginine residues with canavanine in MazF-bs mRNA interferase changes its specificity."
    Ishida Y., Park J.H., Mao L., Yamaguchi Y., Inouye M.
    J. Biol. Chem. 288:7564-7571(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBSTRATE SPECIFICITY.
  6. "Crystal structure of YdcE protein from Bacillus subtilis."
    Gogos A., Mu H., Bahna F., Gomez C.A., Shapiro L.
    Proteins 53:320-322(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 2-116, SUBUNIT.
  7. "Structural basis of mRNA recognition and cleavage by toxin MazF and its regulation by antitoxin MazE in Bacillus subtilis."
    Simanshu D.K., Yamaguchi Y., Park J.H., Inouye M., Patel D.J.
    Mol. Cell 52:447-458(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) IN COMPLEX WITH SUBSTRATE OR MAZE, FUNCTION, SUBUNIT, RNA-BINDING, MUTAGENESIS OF PHE-10; SER-19; GLN-21; ARG-25; ASN-32; THR-48; GLN-50; LYS-53; LEU-56; HIS-59; ARG-71; SER-73; GLU-78; GLN-79 AND ASP-90.
    Strain: 168.

Entry informationi

Entry nameiENDOA_BACSU
AccessioniPrimary (citable) accession number: P96622
Secondary accession number(s): Q797K4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2005
Last sequence update: May 1, 1997
Last modified: June 24, 2015
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Replacing all Arg residues by canavanine yields an enzyme that recognizes a longer consensus sequence UACAUA, thus altering its substrate specificity. Still cleaves between the first and second nucleotides.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.