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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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 375375Ribonuclease DPRO_0000097368Add
BLAST

Proteomic databases

EPDiP09155.
PaxDbiP09155.
PRIDEiP09155.

Interactioni

Protein-protein interaction databases

BioGridi4260338. 11 interactions.
IntActiP09155. 1 interaction.
MINTiMINT-1309170.
STRINGi511145.b1804.

Structurei

Secondary structure

1
375
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Helixi9 – 1911Combined sources
Beta strandi22 – 3211Combined sources
Beta strandi40 – 478Combined sources
Beta strandi52 – 554Combined sources
Helixi57 – 593Combined sources
Helixi64 – 718Combined sources
Beta strandi75 – 817Combined sources
Helixi83 – 9311Combined sources
Beta strandi98 – 1025Combined sources
Helixi103 – 1097Combined sources
Helixi118 – 1269Combined sources
Turni133 – 1364Combined sources
Beta strandi141 – 1433Combined sources
Helixi146 – 15712Combined sources
Helixi159 – 17214Combined sources
Helixi176 – 19116Combined sources
Helixi196 – 2027Combined sources
Helixi206 – 2083Combined sources
Helixi211 – 23121Combined sources
Helixi235 – 2373Combined sources
Helixi241 – 25010Combined sources
Helixi255 – 2606Combined sources
Helixi265 – 28420Combined sources
Helixi287 – 2893Combined sources
Helixi297 – 2993Combined sources
Helixi303 – 32119Combined sources
Helixi325 – 3284Combined sources
Helixi331 – 34111Combined sources
Helixi352 – 3543Combined sources
Helixi356 – 37015Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP09155.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 1691673'-5' exonucleaseUniRule annotationAdd
BLAST
Domaini210 – 28980HRDCUniRule annotationAdd
BLAST

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.
OMAiCAWREEQ.
OrthoDBiEOG6MM1MT.
PhylomeDBiP09155.

Family and domain databases

Gene3Di3.30.420.10. 1 hit.
HAMAPiMF_01899. RNase_D.
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
EntryMethodResolution (Å)ChainPositionsPDBsum
1YT3X-ray1.60A1-375[»]
ProteinModelPortaliP09155.
SMRiP09155. Positions 1-375.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260338. 11 interactions.
IntActiP09155. 1 interaction.
MINTiMINT-1309170.
STRINGi511145.b1804.

Proteomic databases

EPDiP09155.
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.
OMAiCAWREEQ.
OrthoDBiEOG6MM1MT.
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.
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...

Publicationsi

« Hide 'large scale' publications
  1. "Escherichia coli RNase D: sequencing of the rnd structural gene and purification of the overexpressed protein."
    Zhang J., Deutscher M.P.
    Nucleic Acids Res. 16:6265-6278(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-6, FUNCTION.
  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. "The fadD gene of Escherichia coli K12 is located close to rnd at 39.6 min of the chromosomal map and is a new member of the AMP-binding protein family."
    Fulda M., Heinz E., Wolter F.P.
    Mol. Gen. Genet. 242:241-249(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-38.
    Strain: K12.
  6. "Escherichia coli RNase D. Catalytic properties and substrate specificity."
    Cudny H., Zaniewski R., Deutscher M.P.
    J. Biol. Chem. 256:5633-5637(1981) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR.
  7. "Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing."
    Zuo Y., Wang Y., Malhotra A.
    Structure 13:973-984(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).

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: July 6, 2016
This is version 132 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.