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P30014

- RNT_ECOLI

UniProt

P30014 - RNT_ECOLI

Protein

Ribonuclease T

Gene

rnt

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 107 (01 Oct 2014)
      Sequence version 1 (01 Apr 1993)
      Previous versions | rss
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    Functioni

    Trims short 3' overhangs of a variety of RNA species, leaving a one or two nucleotide 3' overhang. Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A). Also appears to be involved in tRNA biosynthesis, especially in strains lacking other exoribonucleases.3 PublicationsUniRule annotation

    Cofactori

    Binds two Mg2+ per subunit. The active form of the enzyme binds two Mg2+ ions in its active site. The first Mg2+ forms only one salt bridge with the protein.4 PublicationsUniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi23 – 231Magnesium 1; catalytic
    Metal bindingi23 – 231Magnesium 2; catalytic
    Metal bindingi25 – 251Magnesium 2; catalytic
    Sitei29 – 291Important for substrate binding and specificity
    Sitei73 – 731Important for substrate binding and specificity
    Sitei77 – 771Important for substrate binding and specificity
    Sitei124 – 1241Important for substrate binding and specificity
    Sitei146 – 1461Important for substrate binding and specificity
    Active sitei181 – 1811Proton donor/acceptor2 PublicationsUniRule annotation
    Metal bindingi181 – 1811Magnesium 2; catalytic
    Metal bindingi186 – 1861Magnesium 2; catalytic

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: EcoCyc
    2. exoribonuclease activity, producing 5'-phosphomonoesters Source: UniProtKB-HAMAP
    3. magnesium ion binding Source: UniProtKB-HAMAP
    4. nucleic acid binding Source: InterPro

    GO - Biological processi

    1. nucleic acid phosphodiester bond hydrolysis Source: GOC
    2. tRNA 3'-end processing Source: EcoCyc

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    tRNA processing

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11547-MONOMER.
    ECOL316407:JW1644-MONOMER.
    MetaCyc:EG11547-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonuclease TUniRule annotation (EC:3.1.13.-UniRule annotation)
    Alternative name(s):
    Exoribonuclease TUniRule annotation
    Short name:
    RNase TUniRule annotation
    Gene namesi
    Name:rntUniRule annotation
    Ordered Locus Names:b1652, JW1644
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11547. rnt.

    Pathology & Biotechi

    Disruption phenotypei

    Required for optimal growth.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi13 – 131R → A: Strongly reduces affinity for RNA. Nearly abolishes enzyme activity. 1 Publication
    Mutagenesisi15 – 151R → A: Strongly reduces affinity for RNA. 1 Publication
    Mutagenesisi23 – 231D → A: Nearly abolishes enzyme activity. 1 Publication
    Mutagenesisi25 – 251E → A: Nearly abolishes enzyme activity. 1 Publication
    Mutagenesisi29 – 291F → A: Abolishes enzyme activity; when associated with A-73 and A-77. 1 Publication
    Mutagenesisi73 – 731E → A: Reduces enzyme activity. Abolishes enzyme activity; when associated with A-29 and A-77. 1 Publication
    Mutagenesisi77 – 771F → A: Abolishes enzyme activity; when associated with A-29 and A-73. 1 Publication
    Mutagenesisi108 – 1081K → A: Strongly reduces affinity for RNA. 1 Publication
    Mutagenesisi114 – 1141R → A: Strongly reduces affinity for RNA. 1 Publication
    Mutagenesisi124 – 1241F → A: Abolishes enzyme activity; when associated with A-146. 1 Publication
    Mutagenesisi139 – 1391K → A: Reduces affinity for RNA. 1 Publication
    Mutagenesisi146 – 1461F → A: Abolishes enzyme activity; when associated with A-124. 1 Publication
    Mutagenesisi150 – 1501D → A: Nearly abolishes enzyme activity. 1 Publication
    Mutagenesisi181 – 1811H → A: Nearly abolishes enzyme activity. 1 Publication
    Mutagenesisi186 – 1861D → A: Nearly abolishes enzyme activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 215215Ribonuclease TPRO_0000208960Add
    BLAST

    Proteomic databases

    PaxDbiP30014.
    PRIDEiP30014.

    Expressioni

    Gene expression databases

    GenevestigatoriP30014.

    Interactioni

    Subunit structurei

    Homodimer.2 PublicationsUniRule annotation

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    aceFP069591EBI-557418,EBI-542707

    Protein-protein interaction databases

    DIPiDIP-10734N.
    IntActiP30014. 2 interactions.
    MINTiMINT-1248458.
    STRINGi511145.b1652.

    Structurei

    Secondary structure

    1
    215
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 73
    Helixi10 – 134
    Turni14 – 163
    Beta strandi17 – 2913
    Turni31 – 333
    Beta strandi36 – 4611
    Beta strandi48 – 503
    Beta strandi52 – 6211
    Helixi72 – 787
    Helixi85 – 873
    Helixi92 – 10716
    Turni108 – 1114
    Beta strandi114 – 1196
    Turni120 – 1223
    Helixi123 – 13513
    Beta strandi143 – 1508
    Helixi151 – 1599
    Helixi164 – 1718
    Turni177 – 1815
    Helixi183 – 20321
    Helixi211 – 2133

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2IS3X-ray3.10A/B/C/D1-215[»]
    3NGYX-ray2.20A/B/C/D1-215[»]
    3NGZX-ray2.10A/B1-215[»]
    3NH0X-ray2.30A/B1-215[»]
    3NH1X-ray2.11A/B/C/D1-215[»]
    3NH2X-ray2.30A/B/E/F1-215[»]
    3V9SX-ray2.10A/B1-215[»]
    3V9UX-ray2.30A/B/C/D1-215[»]
    3V9WX-ray1.70A/B/C/D1-215[»]
    3V9XX-ray1.90A/B/C/D1-215[»]
    3V9ZX-ray1.80A/B1-215[»]
    3VA0X-ray2.20A/B1-215[»]
    3VA3X-ray2.71A/B1-215[»]
    4KAZX-ray1.90A1-215[»]
    4KB0X-ray2.00A/B1-215[»]
    4KB1X-ray1.80A/B1-215[»]
    ProteinModelPortaliP30014.
    SMRiP30014. Positions 7-215.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP30014.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini20 – 194175ExonucleaseUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the RNase T family.UniRule annotation
    Contains 1 exonuclease domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0847.
    HOGENOMiHOG000279358.
    KOiK03683.
    OMAiLFCYMVN.
    OrthoDBiEOG6QG8H4.
    PhylomeDBiP30014.

    Family and domain databases

    Gene3Di3.30.420.10. 1 hit.
    HAMAPiMF_00157. RNase_T.
    InterProiIPR006055. Exonuclease.
    IPR013520. Exonuclease_RNaseT/DNA_pol3.
    IPR005987. RNase_T.
    IPR012337. RNaseH-like_dom.
    [Graphical view]
    PfamiPF00929. RNase_T. 1 hit.
    [Graphical view]
    SMARTiSM00479. EXOIII. 1 hit.
    [Graphical view]
    SUPFAMiSSF53098. SSF53098. 1 hit.
    TIGRFAMsiTIGR01298. RNaseT. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P30014-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSDNAQLTGL CDRFRGFYPV VIDVETAGFN AKTDALLEIA AITLKMDEQG    50
    WLMPDTTLHF HVEPFVGANL QPEALAFNGI DPNDPDRGAV SEYEALHEIF 100
    KVVRKGIKAS GCNRAIMVAH NANFDHSFMM AAAERASLKR NPFHPFATFD 150
    TAALAGLALG QTVLSKACQT AGMDFDSTQA HSALYDTERT AVLFCEIVNR 200
    WKRLGGWPLS AAEEV 215
    Length:215
    Mass (Da):23,523
    Last modified:April 1, 1993 - v1
    Checksum:i502C1CCEFABF4B05
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L01622 Genomic DNA. Translation: AAC37008.1.
    U00096 Genomic DNA. Translation: AAC74724.1.
    AP009048 Genomic DNA. Translation: BAA15418.2.
    PIRiA45065.
    RefSeqiNP_416169.1. NC_000913.3.
    YP_489916.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74724; AAC74724; b1652.
    BAA15418; BAA15418; BAA15418.
    GeneIDi12931273.
    946159.
    KEGGiecj:Y75_p1629.
    eco:b1652.
    PATRICi32118606. VBIEscCol129921_1723.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L01622 Genomic DNA. Translation: AAC37008.1 .
    U00096 Genomic DNA. Translation: AAC74724.1 .
    AP009048 Genomic DNA. Translation: BAA15418.2 .
    PIRi A45065.
    RefSeqi NP_416169.1. NC_000913.3.
    YP_489916.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2IS3 X-ray 3.10 A/B/C/D 1-215 [» ]
    3NGY X-ray 2.20 A/B/C/D 1-215 [» ]
    3NGZ X-ray 2.10 A/B 1-215 [» ]
    3NH0 X-ray 2.30 A/B 1-215 [» ]
    3NH1 X-ray 2.11 A/B/C/D 1-215 [» ]
    3NH2 X-ray 2.30 A/B/E/F 1-215 [» ]
    3V9S X-ray 2.10 A/B 1-215 [» ]
    3V9U X-ray 2.30 A/B/C/D 1-215 [» ]
    3V9W X-ray 1.70 A/B/C/D 1-215 [» ]
    3V9X X-ray 1.90 A/B/C/D 1-215 [» ]
    3V9Z X-ray 1.80 A/B 1-215 [» ]
    3VA0 X-ray 2.20 A/B 1-215 [» ]
    3VA3 X-ray 2.71 A/B 1-215 [» ]
    4KAZ X-ray 1.90 A 1-215 [» ]
    4KB0 X-ray 2.00 A/B 1-215 [» ]
    4KB1 X-ray 1.80 A/B 1-215 [» ]
    ProteinModelPortali P30014.
    SMRi P30014. Positions 7-215.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10734N.
    IntActi P30014. 2 interactions.
    MINTi MINT-1248458.
    STRINGi 511145.b1652.

    Proteomic databases

    PaxDbi P30014.
    PRIDEi P30014.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74724 ; AAC74724 ; b1652 .
    BAA15418 ; BAA15418 ; BAA15418 .
    GeneIDi 12931273.
    946159.
    KEGGi ecj:Y75_p1629.
    eco:b1652.
    PATRICi 32118606. VBIEscCol129921_1723.

    Organism-specific databases

    EchoBASEi EB1509.
    EcoGenei EG11547. rnt.

    Phylogenomic databases

    eggNOGi COG0847.
    HOGENOMi HOG000279358.
    KOi K03683.
    OMAi LFCYMVN.
    OrthoDBi EOG6QG8H4.
    PhylomeDBi P30014.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11547-MONOMER.
    ECOL316407:JW1644-MONOMER.
    MetaCyc:EG11547-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P30014.
    PROi P30014.

    Gene expression databases

    Genevestigatori P30014.

    Family and domain databases

    Gene3Di 3.30.420.10. 1 hit.
    HAMAPi MF_00157. RNase_T.
    InterProi IPR006055. Exonuclease.
    IPR013520. Exonuclease_RNaseT/DNA_pol3.
    IPR005987. RNase_T.
    IPR012337. RNaseH-like_dom.
    [Graphical view ]
    Pfami PF00929. RNase_T. 1 hit.
    [Graphical view ]
    SMARTi SM00479. EXOIII. 1 hit.
    [Graphical view ]
    SUPFAMi SSF53098. SSF53098. 1 hit.
    TIGRFAMsi TIGR01298. RNaseT. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and transcriptional analysis of the Escherichia coli rnt gene encoding RNase T."
      Huang S., Deutscher M.P.
      J. Biol. Chem. 267:25609-25613(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY.
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "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.
    5. "RNase T affects Escherichia coli growth and recovery from metabolic stress."
      Padmanabha K.P., Deutscher M.P.
      J. Bacteriol. 173:1376-1381(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
      Strain: CA265.
    6. "Mechanism of action of RNase T. I. Identification of residues required for catalysis, substrate binding, and dimerization."
      Zuo Y., Deutscher M.P.
      J. Biol. Chem. 277:50155-50159(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF ARG-13; ARG-15; ASP-23; GLU-25; LYS-108; ARG-114; LYS-139; ASP-150; HIS-181 AND ASP-186.
    7. "Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover."
      Zuo Y., Zheng H., Wang Y., Chruszcz M., Cymborowski M., Skarina T., Savchenko A., Malhotra A., Minor W.
      Structure 15:417-428(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.10 ANGSTROMS), CATALYTIC ACTIVITY, FUNCTION, COFACTOR, SUBUNIT.
    8. "Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation."
      Hsiao Y.Y., Yang C.C., Lin C.L., Lin J.L., Duh Y., Yuan H.S.
      Nat. Chem. Biol. 7:236-243(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND DNA AS SUBSTRATE ANALOG, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, SITE, COFACTOR, DISRUPTION PHENOTYPE, MUTAGENESIS OF PHE-29; GLU-73; PHE-77; PHE-124 AND PHE-146, SUBUNIT.
    9. "How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes."
      Hsiao Y.Y., Duh Y., Chen Y.P., Wang Y.T., Yuan H.S.
      Nucleic Acids Res. 40:8144-8154(2012) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND DNA AS SUBSTRATE ANALOG, COFACTOR, ACTIVE SITE, CATALYTIC ACTIVITY.

    Entry informationi

    Entry nameiRNT_ECOLI
    AccessioniPrimary (citable) accession number: P30014
    Secondary accession number(s): P76896
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: April 1, 1993
    Last modified: October 1, 2014
    This is version 107 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Member of the DEDD group of RNAses that are characterized by the presence of four acidic residues in the active site. These residues are conserved even when the proteins have highly divergent sequences.

    Keywords - Technical termi

    3D-structure, Complete proteome, 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

    External Data

    Dasty 3