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Protein

Pyrimidine-specific ribonucleoside hydrolase RihB

Gene

rihB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides. Has a low but significant activity for the purine nucleoside xanthosine.

Catalytic activityi

A pyrimidine nucleoside + H2O = D-ribose + a pyrimidine base.

Cofactori

Ca2+Note: Binds 1 Ca2+ ion per monomer.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei11Proton acceptorSequence analysis1
Metal bindingi11Calcium1
Metal bindingi16Calcium1
Metal bindingi124Calcium; via carbonyl oxygen1
Binding sitei227SubstrateBy similarity1
Binding sitei239SubstrateBy similarity1
Metal bindingi240Calcium1

GO - Molecular functioni

  • calcium ion binding Source: EcoCyc
  • identical protein binding Source: EcoCyc
  • purine nucleosidase activity Source: GO_Central
  • uridine nucleosidase activity Source: EcoCyc

GO - Biological processi

  • purine nucleoside catabolic process Source: GO_Central
  • pyrimidine nucleobase metabolic process Source: UniProtKB-HAMAP
  • pyrimidine ribonucleoside catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG12030-MONOMER.
ECOL316407:JW2149-MONOMER.
MetaCyc:EG12030-MONOMER.
BRENDAi3.2.2.8. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyrimidine-specific ribonucleoside hydrolase RihB (EC:3.2.2.8)
Alternative name(s):
Cytidine/uridine-specific hydrolase
Gene namesi
Name:rihB
Synonyms:yeiK
Ordered Locus Names:b2162, JW2149
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12030. rihB.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi82H → N: Increases KM for uridine 2-fold. Increases Kcat 3-fold. 1 Publication1
Mutagenesisi239H → A: Increases KM for uridine 13-fold. No effect on Kcat. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002068241 – 313Pyrimidine-specific ribonucleoside hydrolase RihBAdd BLAST313

Proteomic databases

PaxDbiP33022.
PRIDEiP33022.

Interactioni

Subunit structurei

Homotetramer.1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4261071. 3 interactors.
IntActiP33022. 5 interactors.
STRINGi511145.b2162.

Structurei

Secondary structure

1313
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 10Combined sources7
Helixi14 – 25Combined sources12
Beta strandi29 – 36Combined sources8
Beta strandi38 – 41Combined sources4
Helixi43 – 56Combined sources14
Beta strandi63 – 65Combined sources3
Beta strandi71 – 73Combined sources3
Helixi79 – 82Combined sources4
Turni83 – 85Combined sources3
Helixi104 – 114Combined sources11
Beta strandi119 – 123Combined sources5
Helixi128 – 136Combined sources9
Helixi138 – 143Combined sources6
Beta strandi144 – 150Combined sources7
Beta strandi158 – 162Combined sources5
Helixi165 – 168Combined sources4
Helixi171 – 178Combined sources8
Beta strandi184 – 187Combined sources4
Helixi189 – 192Combined sources4
Helixi193 – 195Combined sources3
Helixi199 – 208Combined sources10
Helixi210 – 231Combined sources22
Beta strandi234 – 237Combined sources4
Helixi241 – 248Combined sources8
Helixi250 – 252Combined sources3
Beta strandi253 – 258Combined sources6
Beta strandi260 – 262Combined sources3
Turni268 – 271Combined sources4
Beta strandi273 – 275Combined sources3
Beta strandi287 – 293Combined sources7
Helixi295 – 307Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Q8FX-ray1.70A/B/C/D1-313[»]
3B9XX-ray2.30A/B/C/D1-313[»]
ProteinModelPortaliP33022.
SMRiP33022.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP33022.

Family & Domainsi

Sequence similaritiesi

Belongs to the IUNH family. RihB subfamily.Curated

Phylogenomic databases

eggNOGiENOG4105DU0. Bacteria.
COG1957. LUCA.
HOGENOMiHOG000218839.
InParanoidiP33022.
KOiK10213.
OMAiWIHGDNG.
PhylomeDBiP33022.

Family and domain databases

Gene3Di3.90.245.10. 1 hit.
HAMAPiMF_01433. Pyrim_hydro_RihB. 1 hit.
InterProiIPR015910. I/U_nuclsd_hydro_CS.
IPR023186. Inosine/uridine_hydrolase.
IPR001910. Inosine/uridine_hydrolase_dom.
IPR022977. Pyrim_hydro_RihB.
[Graphical view]
PANTHERiPTHR12304. PTHR12304. 1 hit.
PfamiPF01156. IU_nuc_hydro. 1 hit.
[Graphical view]
SUPFAMiSSF53590. SSF53590. 1 hit.
PROSITEiPS01247. IUNH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P33022-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKRKIILDC DPGHDDAIAI MMAAKHPAID LLGITIVAGN QTLDKTLING
60 70 80 90 100
LNVCQKLEIN VPVYAGMPQP IMRQQIVADN IHGETGLDGP VFEPLTRQAE
110 120 130 140 150
STHAVKYIID TLMASDGDIT LVPVGPLSNI AVAMRMQPAI LPKIREIVLM
160 170 180 190 200
GGAYGTGNFT PSAEFNIFAD PEAARVVFTS GVPLVMMGLD LTNQTVCTPD
210 220 230 240 250
VIARMERAGG PAGELFSDIM NFTLKTQFEN YGLAGGPVHD ATCIGYLINP
260 270 280 290 300
DGIKTQEMYV EVDVNSGPCY GRTVCDELGV LGKPANTKVG ITIDTDWFWG
310
LVEECVRGYI KTH
Length:313
Mass (Da):33,748
Last modified:February 1, 1994 - v1
Checksum:iBA3FA8B975474B28
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00007 Genomic DNA. Translation: AAA60514.1.
U00096 Genomic DNA. Translation: AAC75223.1.
AP009048 Genomic DNA. Translation: BAE76639.1.
PIRiA64985.
RefSeqiNP_416667.1. NC_000913.3.
WP_000415429.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75223; AAC75223; b2162.
BAE76639; BAE76639; BAE76639.
GeneIDi946646.
KEGGiecj:JW2149.
eco:b2162.
PATRICi32119673. VBIEscCol129921_2247.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00007 Genomic DNA. Translation: AAA60514.1.
U00096 Genomic DNA. Translation: AAC75223.1.
AP009048 Genomic DNA. Translation: BAE76639.1.
PIRiA64985.
RefSeqiNP_416667.1. NC_000913.3.
WP_000415429.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Q8FX-ray1.70A/B/C/D1-313[»]
3B9XX-ray2.30A/B/C/D1-313[»]
ProteinModelPortaliP33022.
SMRiP33022.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261071. 3 interactors.
IntActiP33022. 5 interactors.
STRINGi511145.b2162.

Proteomic databases

PaxDbiP33022.
PRIDEiP33022.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75223; AAC75223; b2162.
BAE76639; BAE76639; BAE76639.
GeneIDi946646.
KEGGiecj:JW2149.
eco:b2162.
PATRICi32119673. VBIEscCol129921_2247.

Organism-specific databases

EchoBASEiEB1965.
EcoGeneiEG12030. rihB.

Phylogenomic databases

eggNOGiENOG4105DU0. Bacteria.
COG1957. LUCA.
HOGENOMiHOG000218839.
InParanoidiP33022.
KOiK10213.
OMAiWIHGDNG.
PhylomeDBiP33022.

Enzyme and pathway databases

BioCyciEcoCyc:EG12030-MONOMER.
ECOL316407:JW2149-MONOMER.
MetaCyc:EG12030-MONOMER.
BRENDAi3.2.2.8. 2026.

Miscellaneous databases

EvolutionaryTraceiP33022.
PROiP33022.

Family and domain databases

Gene3Di3.90.245.10. 1 hit.
HAMAPiMF_01433. Pyrim_hydro_RihB. 1 hit.
InterProiIPR015910. I/U_nuclsd_hydro_CS.
IPR023186. Inosine/uridine_hydrolase.
IPR001910. Inosine/uridine_hydrolase_dom.
IPR022977. Pyrim_hydro_RihB.
[Graphical view]
PANTHERiPTHR12304. PTHR12304. 1 hit.
PfamiPF01156. IU_nuc_hydro. 1 hit.
[Graphical view]
SUPFAMiSSF53590. SSF53590. 1 hit.
PROSITEiPS01247. IUNH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRIHB_ECOLI
AccessioniPrimary (citable) accession number: P33022
Secondary accession number(s): Q2MAR7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: February 1, 1994
Last modified: November 2, 2016
This is version 120 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, 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.