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UniProtKB - P28619 (RNPH_BACSU)

Entry version 132 (02 Dec 2020)
Sequence version 1 (01 Dec 1992)
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Protein

Ribonuclease PH

Gene

rph

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:4 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

Phosphorolytic 3'-5' exoribonuclease that plays an important role in tRNA 3'-end maturation. Removes nucleotide residues following the 3'-CCA terminus of tRNAs; can also add nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates, but this may not be physiologically important. Probably plays a role in initiation of 16S rRNA degradation (leading to ribosome degradation) during starvation. Plays a role in the secondary pathway of 23S rRNA 3' end maturation (PubMed:19880604).UniRule annotation1 Publication

Miscellaneous

Sulfate ions in the crystal structure may represent the inorganic phosphate substrate.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei86Phosphate (substrate) bindingUniRule annotation1

<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

Complete GO annotation on QuickGO ...

GO - Biological processi

  • rRNA 3'-end processing Source: UniProtKB
  • rRNA catabolic process Source: GO_Central
  • tRNA processing Source: UniProtKB-UniRule
Complete GO annotation on QuickGO ...

<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 functionNucleotidyltransferase, RNA-binding, Transferase, tRNA-binding
Biological processrRNA processing, tRNA processing

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		BSUB:BSU28370-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%5Fand%5Ftaxonomy%5Fsection">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 PHUniRule annotation (EC:2.7.7.56UniRule annotation)
Short name:
RNase PHUniRule annotation
Alternative name(s):
tRNA nucleotidyltransferaseUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:rphUniRule annotation
Ordered Locus Names:BSU28370
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiBacillus subtilis (strain 168)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri224308 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Correct processing of the 3' end of 23S rRNA no longer occurs in the absence of mrnC.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi68 – 76RATNQRTIR → QATNQQTIQ: Protein crystallizes as a dimer. 1 Publication9

<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 or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001398691 – 245Ribonuclease PHAdd BLAST245

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P28619

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

More...PaxDbi		P28619

PRoteomics IDEntifications database

More...PRIDEi		P28619

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homohexameric ring arranged as a trimer of dimers (PubMed:14767080). It has been suggested that the active form is the dimer which binds tRNA and that the hexameric form protects the substrate recognition loop (approximately residues 65-82) from proteolysis (PubMed:14767080).

UniRule annotation1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		224308.BSU28370

<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

1245
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

More...SMRi		P28619

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		P28619

<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

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni124 – 126Phosphate (substrate) bindingUniRule annotation1 Publication3

<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 PH family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0689, Bacteria

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P28619

Identification of Orthologs from Complete Genome Data

More...OMAi		KGKGQGW

Database for complete collections of gene phylogenies

More...PhylomeDBi		P28619

Family and domain databases

Conserved Domains Database

More...CDDi		cd11362, RNase_PH_bact, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.230.70, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_00564, RNase_PH, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001247, ExoRNase_PH_dom1
IPR015847, ExoRNase_PH_dom2
IPR036345, ExoRNase_PH_dom2_sf
IPR027408, PNPase/RNase_PH_dom_sf
IPR020568, Ribosomal_S5_D2-typ_fold
IPR002381, RNase_PH_bac-type
IPR018336, RNase_PH_CS

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01138, RNase_PH, 1 hit
PF03725, RNase_PH_C, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF54211, SSF54211, 1 hit
SSF55666, SSF55666, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR01966, RNasePH, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS01277, RIBONUCLEASE_PH, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P28619-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MRHDGRQHDE LRPITFDLDF ISHPEGSVLI TAGNTKVICN ASVEDRVPPF 
        60         70         80         90        100
LRGGGKGWIT AEYSMLPRAT NQRTIRESSK GKISGRTMEI QRLIGRALRA 
       110        120        130        140        150
VVDLEKLGER TIWIDCDVIQ ADGGTRTASI TGAFLAMAIA IGKLIKAGTI 
       160        170        180        190        200
KTNPITDFLA AISVGIDKEQ GILLDLNYEE DSSAEVDMNV IMTGSGRFVE 
       210        220        230        240 
LQGTGEEATF SREDLNGLLG LAEKGIQELI DKQKEVLGDS LPELK
Length:245
Mass (Da):26,681
Last modified:December 1, 1992 - 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:iD180DB086A5316B8
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
M85163 Genomic DNA Translation: AAA22705.1
Z75208 Genomic DNA Translation: CAA99554.1
AL009126 Genomic DNA Translation: CAB14797.1

Protein sequence database of the Protein Information Resource

More...PIRi		A44914

NCBI Reference Sequences

More...RefSeqi		NP_390715.1, NC_000964.3
WP_003246039.1, NZ_JNCM01000036.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CAB14797; CAB14797; BSU28370

Database of genes from NCBI RefSeq genomes

More...GeneIDi		51992458
937463

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		bsu:BSU28370

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|224308.179.peg.3082

<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
M85163 Genomic DNA Translation: AAA22705.1
Z75208 Genomic DNA Translation: CAA99554.1
AL009126 Genomic DNA Translation: CAB14797.1
PIRiA44914
RefSeqiNP_390715.1, NC_000964.3
WP_003246039.1, NZ_JNCM01000036.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OYPX-ray2.76A/B/C/D/E/F1-245[»]
1OYRX-ray3.10A/B/C/D/E/F1-245[»]
1OYSX-ray2.40A1-245[»]
SMRiP28619
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU28370

Proteomic databases

jPOSTiP28619
PaxDbiP28619
PRIDEiP28619

Genome annotation databases

EnsemblBacteriaiCAB14797; CAB14797; BSU28370
GeneIDi51992458
937463
KEGGibsu:BSU28370
PATRICifig|224308.179.peg.3082

Phylogenomic databases

eggNOGiCOG0689, Bacteria
InParanoidiP28619
OMAiKGKGQGW
PhylomeDBiP28619

Enzyme and pathway databases

BioCyciBSUB:BSU28370-MONOMER

Miscellaneous databases

EvolutionaryTraceiP28619

Protein Ontology

More...PROi		PR:P28619

Family and domain databases

CDDicd11362, RNase_PH_bact, 1 hit
Gene3Di3.30.230.70, 1 hit
HAMAPiMF_00564, RNase_PH, 1 hit
InterProiView protein in InterPro
IPR001247, ExoRNase_PH_dom1
IPR015847, ExoRNase_PH_dom2
IPR036345, ExoRNase_PH_dom2_sf
IPR027408, PNPase/RNase_PH_dom_sf
IPR020568, Ribosomal_S5_D2-typ_fold
IPR002381, RNase_PH_bac-type
IPR018336, RNase_PH_CS
PfamiView protein in Pfam
PF01138, RNase_PH, 1 hit
PF03725, RNase_PH_C, 1 hit
SUPFAMiSSF54211, SSF54211, 1 hit
SSF55666, SSF55666, 1 hit
TIGRFAMsiTIGR01966, RNasePH, 1 hit
PROSITEiView protein in PROSITE
PS01277, RIBONUCLEASE_PH, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		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 nameiRNPH_BACSU
<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: P28619
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 1992
Last sequence update: December 1, 1992
Last modified: December 2, 2020
This is version 132 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, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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