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Protein

Ribonuclease D

Gene

rnd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides.UniRule annotation2 Publications

Catalytic activityi

Exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides.UniRule annotation1 Publication

Cofactori

a divalent metal cationUniRule annotation1 Publication

GO - Molecular functioni

  • 3'-5' exonuclease activity Source: InterPro
  • nucleic acid binding Source: InterPro
  • nucleotide binding Source: InterPro
  • ribonuclease activity Source: EcoCyc
  • ribonuclease D activity Source: UniProtKB-HAMAP

GO - Biological processi

  • tRNA 3'-end processing Source: UniProtKB-HAMAP
  • tRNA processing Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

tRNA processing

Enzyme and pathway databases

BioCyciEcoCyc:EG10858-MONOMER.
ECOL316407:JW1793-MONOMER.
MetaCyc:EG10858-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonuclease DUniRule annotation (EC:3.1.13.5UniRule annotation)
Short name:
RNase DUniRule annotation
Gene namesi
Name:rndUniRule annotation
Ordered Locus Names:b1804, JW1793
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10858. rnd.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000973681 – 375Ribonuclease DAdd BLAST375

Proteomic databases

PaxDbiP09155.
PRIDEiP09155.

Interactioni

Protein-protein interaction databases

BioGridi4260338. 11 interactors.
IntActiP09155. 1 interactor.
MINTiMINT-1309170.
STRINGi511145.b1804.

Structurei

Secondary structure

1375
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 6Combined sources3
Helixi9 – 19Combined sources11
Beta strandi22 – 32Combined sources11
Beta strandi40 – 47Combined sources8
Beta strandi52 – 55Combined sources4
Helixi57 – 59Combined sources3
Helixi64 – 71Combined sources8
Beta strandi75 – 81Combined sources7
Helixi83 – 93Combined sources11
Beta strandi98 – 102Combined sources5
Helixi103 – 109Combined sources7
Helixi118 – 126Combined sources9
Turni133 – 136Combined sources4
Beta strandi141 – 143Combined sources3
Helixi146 – 157Combined sources12
Helixi159 – 172Combined sources14
Helixi176 – 191Combined sources16
Helixi196 – 202Combined sources7
Helixi206 – 208Combined sources3
Helixi211 – 231Combined sources21
Helixi235 – 237Combined sources3
Helixi241 – 250Combined sources10
Helixi255 – 260Combined sources6
Helixi265 – 284Combined sources20
Helixi287 – 289Combined sources3
Helixi297 – 299Combined sources3
Helixi303 – 321Combined sources19
Helixi325 – 328Combined sources4
Helixi331 – 341Combined sources11
Helixi352 – 354Combined sources3
Helixi356 – 370Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YT3X-ray1.60A1-375[»]
ProteinModelPortaliP09155.
SMRiP09155.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP09155.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 1693'-5' exonucleaseUniRule annotationAdd BLAST167
Domaini210 – 289HRDCUniRule annotationAdd BLAST80

Sequence similaritiesi

Belongs to the RNase D family.UniRule annotation
Contains 1 3'-5' exonuclease domain.UniRule annotation
Contains 1 HRDC domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105ZIE. Bacteria.
COG0349. LUCA.
HOGENOMiHOG000277560.
InParanoidiP09155.
KOiK03684.
OMAiITDWAPF.
PhylomeDBiP09155.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_01899. RNase_D. 1 hit.
InterProiIPR002562. 3'-5'_exonuclease_dom.
IPR010997. HRDC-like.
IPR002121. HRDC_dom.
IPR006292. RNase_D.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF01612. DNA_pol_A_exo1. 1 hit.
PF00570. HRDC. 1 hit.
[Graphical view]
SMARTiSM00474. 35EXOc. 1 hit.
SM00341. HRDC. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 2 hits.
SSF53098. SSF53098. 1 hit.
TIGRFAMsiTIGR01388. rnd. 1 hit.
PROSITEiPS50967. HRDC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P09155-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNYQMITTDD ALASLCEAVR AFPAIALDTE FVRTRTYYPQ LGLIQLFDGE
60 70 80 90 100
HLALIDPLGI TDWSPLKAIL RDPSITKFLH AGSEDLEVFL NVFGELPQPL
110 120 130 140 150
IDTQILAAFC GRPMSWGFAS MVEEYSGVTL DKSESRTDWL ARPLTERQCE
160 170 180 190 200
YAAADVWYLL PITAKLMVET EASGWLPAAL DECRLMQMRR QEVVAPEDAW
210 220 230 240 250
RDITNAWQLR TRQLACLQLL ADWRLRKARE RDLAVNFVVR EEHLWSVARY
260 270 280 290 300
MPGSLGELDS LGLSGSEIRF HGKTLLALVE KAQTLPEDAL PQPMLNLMDM
310 320 330 340 350
PGYRKAFKAI KSLITDVSET HKISAELLAS RRQINQLLNW HWKLKPQNNL
360 370
PELISGWRGE LMAEALHNLL QEYPQ
Length:375
Mass (Da):42,734
Last modified:July 1, 1989 - v1
Checksum:iAC0E6D3883712BAE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07055 Genomic DNA. Translation: CAA30098.1.
U00096 Genomic DNA. Translation: AAC74874.1.
AP009048 Genomic DNA. Translation: BAA15599.1.
X70994 Genomic DNA. Translation: CAA50322.1.
PIRiS01223. NRECD.
RefSeqiNP_416318.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC74874; AAC74874; b1804.
BAA15599; BAA15599; BAA15599.
GeneIDi946328.
KEGGiecj:JW1793.
eco:b1804.
PATRICi32118925. VBIEscCol129921_1880.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07055 Genomic DNA. Translation: CAA30098.1.
U00096 Genomic DNA. Translation: AAC74874.1.
AP009048 Genomic DNA. Translation: BAA15599.1.
X70994 Genomic DNA. Translation: CAA50322.1.
PIRiS01223. NRECD.
RefSeqiNP_416318.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YT3X-ray1.60A1-375[»]
ProteinModelPortaliP09155.
SMRiP09155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260338. 11 interactors.
IntActiP09155. 1 interactor.
MINTiMINT-1309170.
STRINGi511145.b1804.

Proteomic databases

PaxDbiP09155.
PRIDEiP09155.

Protocols and materials databases

DNASUi946328.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74874; AAC74874; b1804.
BAA15599; BAA15599; BAA15599.
GeneIDi946328.
KEGGiecj:JW1793.
eco:b1804.
PATRICi32118925. VBIEscCol129921_1880.

Organism-specific databases

EchoBASEiEB0851.
EcoGeneiEG10858. rnd.

Phylogenomic databases

eggNOGiENOG4105ZIE. Bacteria.
COG0349. LUCA.
HOGENOMiHOG000277560.
InParanoidiP09155.
KOiK03684.
OMAiITDWAPF.
PhylomeDBiP09155.

Enzyme and pathway databases

BioCyciEcoCyc:EG10858-MONOMER.
ECOL316407:JW1793-MONOMER.
MetaCyc:EG10858-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP09155.
PROiP09155.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_01899. RNase_D. 1 hit.
InterProiIPR002562. 3'-5'_exonuclease_dom.
IPR010997. HRDC-like.
IPR002121. HRDC_dom.
IPR006292. RNase_D.
IPR012337. RNaseH-like_dom.
[Graphical view]
PfamiPF01612. DNA_pol_A_exo1. 1 hit.
PF00570. HRDC. 1 hit.
[Graphical view]
SMARTiSM00474. 35EXOc. 1 hit.
SM00341. HRDC. 1 hit.
[Graphical view]
SUPFAMiSSF47819. SSF47819. 2 hits.
SSF53098. SSF53098. 1 hit.
TIGRFAMsiTIGR01388. rnd. 1 hit.
PROSITEiPS50967. HRDC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRND_ECOLI
AccessioniPrimary (citable) accession number: P09155
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: November 2, 2016
This is version 134 of the entry and version 1 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.