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Protein

Oligoribonuclease

Gene

orn

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

Functioni

3'-to-5' exoribonuclease specific for small oligoribonucleotides 2 to 5 nucleotides in length, as well as small (2 to 5 nucleotides) ssDNA oligomers. Probably responsible for the final step in mRNA degradation.3 Publications

Enzyme regulationi

Inhibited by adenosine 3',5'-bisphosphate (PAP).1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi12 – 121Zinc
Metal bindingi14 – 141Zinc
Active sitei129 – 1291Sequence analysis
Metal bindingi163 – 1631Zinc

GO - Molecular functioni

  • 3'-5'-exoribonuclease activity Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • nucleic acid binding Source: InterPro
  • oligoribonucleotidase activity Source: EcoCyc
  • single-stranded DNA 3'-5' exodeoxyribonuclease activity Source: EcoCyc

GO - Biological processi

  • DNA metabolic process Source: GOC
  • nucleic acid phosphodiester bond hydrolysis Source: GOC
  • RNA catabolic process Source: EcoCyc
  • RNA phosphodiester bond hydrolysis Source: GOC
  • RNA phosphodiester bond hydrolysis, exonucleolytic Source: GOC
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:G7842-MONOMER.
ECOL316407:JW5740-MONOMER.
MetaCyc:G7842-MONOMER.
BRENDAi3.1.13.3. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Oligoribonuclease (EC:3.1.-.-)
Gene namesi
Name:orn
Synonyms:o204a, yjeR
Ordered Locus Names:b4162, JW5740
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12480. orn.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Essential. In depletion experiments the level of oligonucleotides is elevated and that of mononucleotides is severly reduced compared to wild-type.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 181180OligoribonucleasePRO_0000111033Add
BLAST

Proteomic databases

EPDiP0A784.
PaxDbiP0A784.
PRIDEiP0A784.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

DIPiDIP-10412N.
STRINGi511145.b4162.

Structurei

Secondary structure

1
181
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi4 – 63Combined sources
Beta strandi8 – 1811Combined sources
Turni20 – 223Combined sources
Beta strandi25 – 339Combined sources
Beta strandi39 – 479Combined sources
Helixi52 – 554Combined sources
Helixi60 – 689Combined sources
Helixi71 – 777Combined sources
Helixi82 – 9312Combined sources
Turni94 – 963Combined sources
Beta strandi104 – 1085Combined sources
Helixi109 – 11911Combined sources
Helixi121 – 1266Combined sources
Beta strandi131 – 1333Combined sources
Helixi135 – 14410Combined sources
Helixi146 – 1516Combined sources
Helixi160 – 17718Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YTAX-ray2.20A/B/C/D2-181[»]
2IGIX-ray1.70A/B2-181[»]
ProteinModelPortaliP0A784.
SMRiP0A784. Positions 2-181.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A784.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini8 – 171164ExonucleaseAdd
BLAST

Sequence similaritiesi

Belongs to the oligoribonuclease family.Curated
Contains 1 exonuclease domain.Curated

Phylogenomic databases

eggNOGiENOG4108RBP. Bacteria.
COG1949. LUCA.
HOGENOMiHOG000246596.
InParanoidiP0A784.
KOiK13288.
OMAiAFFHYRN.
OrthoDBiEOG6Z9B51.
PhylomeDBiP0A784.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_00045. Oligoribonuclease.
InterProiIPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR022894. Oligoribonuclease.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00929. RNase_T. 1 hit.
[Graphical view]
SMARTiSM00479. EXOIII. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A784-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSANENNLIW IDLEMTGLDP ERDRIIEIAT LVTDANLNIL AEGPTIAVHQ
60 70 80 90 100
SDEQLALMDD WNVRTHTASG LVERVKASTM GDREAELATL EFLKQWVPAG
110 120 130 140 150
KSPICGNSIG QDRRFLFKYM PELEAYFHYR YLDVSTLKEL ARRWKPEILD
160 170 180
GFTKQGTHQA MDDIRESVAE LAYYREHFIK L
Length:181
Mass (Da):20,816
Last modified:January 23, 2007 - v2
Checksum:i57A5C7D500C4502F
GO

Sequence cautioni

The sequence AAA97061.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U14003 Genomic DNA. Translation: AAA97061.1. Different initiation.
U00096 Genomic DNA. Translation: AAC77122.2.
AP009048 Genomic DNA. Translation: BAE78166.1.
PIRiS56390.
RefSeqiNP_418586.4. NC_000913.3.
WP_001295188.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77122; AAC77122; b4162.
BAE78166; BAE78166; BAE78166.
GeneIDi948675.
KEGGiecj:JW5740.
eco:b4162.
PATRICi32123897. VBIEscCol129921_4296.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U14003 Genomic DNA. Translation: AAA97061.1. Different initiation.
U00096 Genomic DNA. Translation: AAC77122.2.
AP009048 Genomic DNA. Translation: BAE78166.1.
PIRiS56390.
RefSeqiNP_418586.4. NC_000913.3.
WP_001295188.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1YTAX-ray2.20A/B/C/D2-181[»]
2IGIX-ray1.70A/B2-181[»]
ProteinModelPortaliP0A784.
SMRiP0A784. Positions 2-181.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-10412N.
STRINGi511145.b4162.

Proteomic databases

EPDiP0A784.
PaxDbiP0A784.
PRIDEiP0A784.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77122; AAC77122; b4162.
BAE78166; BAE78166; BAE78166.
GeneIDi948675.
KEGGiecj:JW5740.
eco:b4162.
PATRICi32123897. VBIEscCol129921_4296.

Organism-specific databases

EchoBASEiEB2373.
EcoGeneiEG12480. orn.

Phylogenomic databases

eggNOGiENOG4108RBP. Bacteria.
COG1949. LUCA.
HOGENOMiHOG000246596.
InParanoidiP0A784.
KOiK13288.
OMAiAFFHYRN.
OrthoDBiEOG6Z9B51.
PhylomeDBiP0A784.

Enzyme and pathway databases

BioCyciEcoCyc:G7842-MONOMER.
ECOL316407:JW5740-MONOMER.
MetaCyc:G7842-MONOMER.
BRENDAi3.1.13.3. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A784.
PROiP0A784.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_00045. Oligoribonuclease.
InterProiIPR013520. Exonuclease_RNaseT/DNA_pol3.
IPR022894. Oligoribonuclease.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF00929. RNase_T. 1 hit.
[Graphical view]
SMARTiSM00479. EXOIII. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Oligoribonuclease is encoded by a highly conserved gene in the 3'-5' exonuclease superfamily."
    Zhang X., Zhu L., Deutscher M.P.
    J. Bacteriol. 180:2779-2781(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-14, POSSIBLE SUBUNIT, FUNCTION.
  5. "Oligoribonuclease is distinct from the other known exoribonucleases of Escherichia coli."
    Yu D., Deutscher M.P.
    J. Bacteriol. 177:4137-4139(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
    Strain: K12.
  6. "Oligoribonuclease is an essential component of the mRNA decay pathway."
    Ghosh S., Deutscher M.P.
    Proc. Natl. Acad. Sci. U.S.A. 96:4372-4377(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
    Strain: K12.
  7. "Oligoribonuclease is a common downstream target of lithium-induced pAp accumulation in Escherichia coli and human cells."
    Mechold U., Ogryzko V., Ngo S., Danchin A.
    Nucleic Acids Res. 34:2364-2373(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ENZYME REGULATION.
  8. "Purification and crystallization of Escherichia coli oligoribonuclease."
    Fiedler T.J., Vincent H.A., Zuo Y., Gavrialov O., Malhotra A.
    Acta Crystallogr. D 60:736-739(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 2-181, SUBUNIT.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.

Entry informationi

Entry nameiORN_ECOLI
AccessioniPrimary (citable) accession number: P0A784
Secondary accession number(s): P39287, P76799, Q2M6E0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: March 16, 2016
This is version 96 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.