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Protein

Ribonuclease D

Gene

rnd

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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-EC

GO - Biological processi

  • tRNA processing Source: EcoCyc

Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease
Biological processtRNA processing

Enzyme and pathway databases

BioCyciEcoCyc:EG10858-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

Organism-specific databases

EcoGeneiEG10858 rnd

Subcellular locationi

GO - Cellular componenti

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, 55 interactors
IntActiP09155, 1 interactor
STRINGi316385.ECDH10B_1942

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

Phylogenomic databases

eggNOGiENOG4105ZIE Bacteria
COG0349 LUCA
HOGENOMiHOG000277560
InParanoidiP09155
KOiK03684
OMAiRSDWLQR
PhylomeDBiP09155

Family and domain databases

Gene3Di3.30.420.10, 1 hit
HAMAPiMF_01899 RNase_D, 1 hit
InterProiView protein in InterPro
IPR002562 3'-5'_exonuclease_dom
IPR010997 HRDC-like_sf
IPR002121 HRDC_dom
IPR006292 RNase_D
IPR012337 RNaseH-like_sf
IPR036397 RNaseH_sf
PfamiView protein in Pfam
PF01612 DNA_pol_A_exo1, 1 hit
PF00570 HRDC, 1 hit
SMARTiView protein in SMART
SM00474 35EXOc, 1 hit
SM00341 HRDC, 1 hit
SUPFAMiSSF47819 SSF47819, 2 hits
SSF53098 SSF53098, 1 hit
TIGRFAMsiTIGR01388 rnd, 1 hit
PROSITEiView protein in PROSITE
PS50967 HRDC, 1 hit

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
WP_001109156.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC74874; AAC74874; b1804
BAA15599; BAA15599; BAA15599
GeneIDi946328
KEGGiecj:JW1793
eco:b1804
PATRICifig|511145.12.peg.1880

Similar proteinsi

Entry informationi

Entry nameiRND_ECOLI
AccessioniPrimary (citable) accession number: P09155
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: March 28, 2018
This is version 144 of the entry and version 1 of the sequence. See 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

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