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P30014

- RNT_ECOLI

UniProt

P30014 - RNT_ECOLI

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Protein

Ribonuclease T

Gene

rnt

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

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
Complete GO annotation...

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.
InParanoidiP30014.
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

        10         20         30         40         50
MSDNAQLTGL CDRFRGFYPV VIDVETAGFN AKTDALLEIA AITLKMDEQG
60 70 80 90 100
WLMPDTTLHF HVEPFVGANL QPEALAFNGI DPNDPDRGAV SEYEALHEIF
110 120 130 140 150
KVVRKGIKAS GCNRAIMVAH NANFDHSFMM AAAERASLKR NPFHPFATFD
160 170 180 190 200
TAALAGLALG QTVLSKACQT AGMDFDSTQA HSALYDTERT AVLFCEIVNR
210
WKRLGGWPLS AAEEV
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.
InParanoidi P30014.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 108 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