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Entry version 151 (08 May 2019)
Sequence version 1 (01 Jul 1989)
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Protein

Ribonuclease D

Gene

rnd

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

Annotation score:3 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

  • Exonucleolytic cleavage that removes extra residues from the 3'-terminus of tRNA to produce 5'-mononucleotides.UniRule annotation1 Publication EC:3.1.13.5

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

a divalent metal cationUniRule annotation1 Publication

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionExonuclease, Hydrolase, Nuclease
Biological processtRNA processing

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG10858-MONOMER
ECOL316407:JW1793-MONOMER
MetaCyc:EG10858-MONOMER

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Ribonuclease DUniRule annotation (EC:3.1.13.5UniRule annotation)
Short name:
RNase DUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rndUniRule annotation
Ordered Locus Names:b1804, JW1793
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

Escherichia coli strain K12 genome database

More...
EcoGenei
EG10858 rnd

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000973681 – 375Ribonuclease DAdd BLAST375

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P09155

PRoteomics IDEntifications database

More...
PRIDEi
P09155

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4260338, 55 interactors

Protein interaction database and analysis system

More...
IntActi
P09155, 1 interactor

STRING: functional protein association networks

More...
STRINGi
511145.b1804

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1375
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P09155

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P09155

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini3 – 1693'-5' exonucleaseUniRule annotationAdd BLAST167
Domaini210 – 289HRDCUniRule annotationAdd BLAST80

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the RNase D family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105ZIE Bacteria
COG0349 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000277560

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P09155

KEGG Orthology (KO)

More...
KOi
K03684

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P09155

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.420.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01899 RNase_D, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View 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

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01612 DNA_pol_A_exo1, 1 hit
PF00570 HRDC, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00474 35EXOc, 1 hit
SM00341 HRDC, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47819 SSF47819, 2 hits
SSF53098 SSF53098, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR01388 rnd, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50967 HRDC, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iAC0E6D3883712BAE
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
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

Protein sequence database of the Protein Information Resource

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PIRi
S01223 NRECD

NCBI Reference Sequences

More...
RefSeqi
NP_416318.1, NC_000913.3
WP_001109156.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC74874; AAC74874; b1804
BAA15599; BAA15599; BAA15599

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
946328

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW1793
eco:b1804

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.1880

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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
WP_001109156.1, NZ_LN832404.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YT3X-ray1.60A1-375[»]
SMRiP09155
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260338, 55 interactors
IntActiP09155, 1 interactor
STRINGi511145.b1804

Proteomic databases

PaxDbiP09155
PRIDEiP09155

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
946328
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB0851
EcoGeneiEG10858 rnd

Phylogenomic databases

eggNOGiENOG4105ZIE Bacteria
COG0349 LUCA
HOGENOMiHOG000277560
InParanoidiP09155
KOiK03684
PhylomeDBiP09155

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP09155

Protein Ontology

More...
PROi
PR:P09155

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

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRND_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P09155
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: May 8, 2019
This is version 151 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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