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Protein

Pyrimidine-specific ribonucleoside hydrolase RihA

Gene

rihA

Organism
Escherichia coli (strain K12)
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

Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.

Miscellaneous

Strictly specific for ribonucleosides.

<p>This subsection of the ‘Function’ section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Subject to catabolite repression.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei240By similarity1

<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

  • calcium ion binding Source: EcoliWiki
  • purine nucleosidase activity Source: GO_Central
  • pyrimidine-5'-nucleotide nucleosidase activity Source: EcoliWiki
  • uridine nucleosidase activity Source: EcoCyc

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 functionGlycosidase, Hydrolase

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G6358-MONOMER
MetaCyc:G6358-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:
Pyrimidine-specific ribonucleoside hydrolase RihA (EC:3.2.-.-)
Alternative name(s):
Cytidine/uridine-specific hydrolase
<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:rihA
Synonyms:ybeK
Ordered Locus Names:b0651, JW0646
<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
EG12701 rihA

<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

  • cytosol Source: GO_Central

<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_00002068131 – 311Pyrimidine-specific ribonucleoside hydrolase RihAAdd BLAST311

Proteomic databases

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

More...
PaxDbi
P41409

PRoteomics IDEntifications database

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PRIDEi
P41409

<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
4261645, 16 interactors

Protein interaction database and analysis system

More...
IntActi
P41409, 15 interactors

STRING: functional protein association networks

More...
STRINGi
316385.ECDH10B_0720

<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

1311
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P41409

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

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SMRi
P41409

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

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MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

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EvolutionaryTracei
P41409

<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

<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 IUNH family. RihA subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105DU0 Bacteria
COG1957 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

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HOGENOMi
HOG000218839

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P41409

KEGG Orthology (KO)

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KOi
K01250

Database for complete collections of gene phylogenies

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PhylomeDBi
P41409

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.90.245.10, 1 hit

HAMAP database of protein families

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HAMAPi
MF_01431 Pyrim_hydro_RihA, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR015910 I/U_nuclsd_hydro_CS
IPR023186 Inosine/uridine_hydrolase
IPR001910 Inosine/uridine_hydrolase_dom
IPR022975 Pyrim_hydro_RihA
IPR036452 Ribo_hydro-like

The PANTHER Classification System

More...
PANTHERi
PTHR12304 PTHR12304, 1 hit

Pfam protein domain database

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Pfami
View protein in Pfam
PF01156 IU_nuc_hydro, 1 hit

Superfamily database of structural and functional annotation

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SUPFAMi
SSF53590 SSF53590, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01247 IUNH, 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>.<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.

P41409-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MALPILLDCD PGHDDAIAIV LALASPELDV KAITSSAGNQ TPEKTLRNVL
60 70 80 90 100
RMLTLLNRTD IPVAGGAVKP LMRELIIADN VHGESGLDGP ALPEPTFAPQ
110 120 130 140 150
NCTAVELMAK TLRESAEPVT IVSTGPQTNV ALLLNSHPEL HSKIARIVIM
160 170 180 190 200
GGAMGLGNWT PAAEFNIYVD PEAAEIVFQS GIPVVMAGLD VTHKAQIHVE
210 220 230 240 250
DTERFRAIGN PVSTIVAELL DFFLEYHKDE KWGFVGAPLH DPCTIAWLLK
260 270 280 290 300
PELFTSVERW VGVETQGKYT QGMTVVDYYY LTGNKPNATV MVDVDRQGFV
310
DLLADRLKFY A
Length:311
Mass (Da):33,823
Last modified:November 1, 1997 - v2
<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:iEEB6CF8C60BABDD4
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U82598 Genomic DNA Translation: AAB40852.1
U00096 Genomic DNA Translation: AAC73752.1
AP009048 Genomic DNA Translation: BAA35303.1
U10981 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

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PIRi
A64800

NCBI Reference Sequences

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RefSeqi
NP_415184.1, NC_000913.3
WP_001207520.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC73752; AAC73752; b0651
BAA35303; BAA35303; BAA35303

Database of genes from NCBI RefSeq genomes

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GeneIDi
945503

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW0646
eco:b0651

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.1617

<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
U82598 Genomic DNA Translation: AAB40852.1
U00096 Genomic DNA Translation: AAC73752.1
AP009048 Genomic DNA Translation: BAA35303.1
U10981 Genomic DNA No translation available.
PIRiA64800
RefSeqiNP_415184.1, NC_000913.3
WP_001207520.1, NZ_LN832404.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

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PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1YOEX-ray1.78A2-311[»]
3G5IX-ray2.10A/B/C/D2-311[»]
ProteinModelPortaliP41409
SMRiP41409
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261645, 16 interactors
IntActiP41409, 15 interactors
STRINGi316385.ECDH10B_0720

Proteomic databases

PaxDbiP41409
PRIDEiP41409

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73752; AAC73752; b0651
BAA35303; BAA35303; BAA35303
GeneIDi945503
KEGGiecj:JW0646
eco:b0651
PATRICifig|1411691.4.peg.1617

Organism-specific databases

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

More...
EchoBASEi
EB2563
EcoGeneiEG12701 rihA

Phylogenomic databases

eggNOGiENOG4105DU0 Bacteria
COG1957 LUCA
HOGENOMiHOG000218839
InParanoidiP41409
KOiK01250
PhylomeDBiP41409

Enzyme and pathway databases

BioCyciEcoCyc:G6358-MONOMER
MetaCyc:G6358-MONOMER

Miscellaneous databases

EvolutionaryTraceiP41409

Protein Ontology

More...
PROi
PR:P41409

Family and domain databases

Gene3Di3.90.245.10, 1 hit
HAMAPiMF_01431 Pyrim_hydro_RihA, 1 hit
InterProiView protein in InterPro
IPR015910 I/U_nuclsd_hydro_CS
IPR023186 Inosine/uridine_hydrolase
IPR001910 Inosine/uridine_hydrolase_dom
IPR022975 Pyrim_hydro_RihA
IPR036452 Ribo_hydro-like
PANTHERiPTHR12304 PTHR12304, 1 hit
PfamiView protein in Pfam
PF01156 IU_nuc_hydro, 1 hit
SUPFAMiSSF53590 SSF53590, 1 hit
PROSITEiView protein in PROSITE
PS01247 IUNH, 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 nameiRIHA_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: P41409
Secondary accession number(s): P77738
<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: November 1, 1995
Last sequence update: November 1, 1997
Last modified: November 7, 2018
This is version 131 of the entry and version 2 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, 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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