RIHB_ECOLI
ID RIHB_ECOLI Reviewed; 313 AA.
AC P33022; Q2MAR7;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1994, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Pyrimidine-specific ribonucleoside hydrolase RihB;
DE EC=3.2.2.8;
DE AltName: Full=Cytidine/uridine-specific hydrolase;
GN Name=rihB; Synonyms=yeiK; OrderedLocusNames=b2162, JW2149;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / BHB2600;
RA Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
RA Church G.M.;
RT "Automated multiplex sequencing of the E.coli genome.";
RL Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP CHARACTERIZATION.
RX PubMed=11027694; DOI=10.1074/jbc.m008300200;
RA Petersen C., Moeller L.B.;
RT "The RihA, RihB, and RihC ribonucleoside hydrolases of Escherichia coli.
RT Substrate specificity, gene expression, and regulation.";
RL J. Biol. Chem. 276:884-894(2001).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH CALCIUM IONS,
RP MUTAGENESIS OF HIS-82 AND HIS-239, AND SUBUNIT.
RX PubMed=15130467; DOI=10.1016/j.str.2004.03.018;
RA Giabbai B., Degano M.;
RT "Crystal structure to 1.7 A of the Escherichia coli pyrimidine nucleoside
RT hydrolase YeiK, a novel candidate for cancer gene therapy.";
RL Structure 12:739-749(2004).
CC -!- FUNCTION: Hydrolyzes cytidine or uridine to ribose and cytosine or
CC uracil, respectively. Has a clear preference for cytidine over uridine.
CC Strictly specific for ribonucleosides. Has a low but significant
CC activity for the purine nucleoside xanthosine.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a pyrimidine ribonucleoside + H2O = a pyrimidine nucleobase +
CC D-ribose; Xref=Rhea:RHEA:56816, ChEBI:CHEBI:15377, ChEBI:CHEBI:26432,
CC ChEBI:CHEBI:47013, ChEBI:CHEBI:141014; EC=3.2.2.8;
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Note=Binds 1 Ca(2+) ion per monomer.;
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:15130467}.
CC -!- SIMILARITY: Belongs to the IUNH family. RihB subfamily. {ECO:0000305}.
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DR EMBL; U00007; AAA60514.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75223.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76639.1; -; Genomic_DNA.
DR PIR; A64985; A64985.
DR RefSeq; NP_416667.1; NC_000913.3.
DR RefSeq; WP_000415429.1; NZ_LN832404.1.
DR PDB; 1Q8F; X-ray; 1.70 A; A/B/C/D=1-313.
DR PDB; 3B9X; X-ray; 2.30 A; A/B/C/D=1-313.
DR PDBsum; 1Q8F; -.
DR PDBsum; 3B9X; -.
DR AlphaFoldDB; P33022; -.
DR SMR; P33022; -.
DR BioGRID; 4261071; 3.
DR IntAct; P33022; 5.
DR STRING; 511145.b2162; -.
DR PaxDb; P33022; -.
DR PRIDE; P33022; -.
DR EnsemblBacteria; AAC75223; AAC75223; b2162.
DR EnsemblBacteria; BAE76639; BAE76639; BAE76639.
DR GeneID; 946646; -.
DR KEGG; ecj:JW2149; -.
DR KEGG; eco:b2162; -.
DR PATRIC; fig|1411691.4.peg.77; -.
DR EchoBASE; EB1965; -.
DR eggNOG; COG1957; Bacteria.
DR HOGENOM; CLU_036838_2_0_6; -.
DR InParanoid; P33022; -.
DR OMA; REKAHEW; -.
DR PhylomeDB; P33022; -.
DR BioCyc; EcoCyc:EG12030-MON; -.
DR BioCyc; MetaCyc:EG12030-MON; -.
DR BRENDA; 3.2.2.8; 2026.
DR EvolutionaryTrace; P33022; -.
DR PRO; PR:P33022; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0005509; F:calcium ion binding; IDA:EcoCyc.
DR GO; GO:0008477; F:purine nucleosidase activity; IBA:GO_Central.
DR GO; GO:0045437; F:uridine nucleosidase activity; IDA:EcoCyc.
DR GO; GO:0006152; P:purine nucleoside catabolic process; IBA:GO_Central.
DR GO; GO:0006206; P:pyrimidine nucleobase metabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0046133; P:pyrimidine ribonucleoside catabolic process; IMP:EcoCyc.
DR Gene3D; 3.90.245.10; -; 1.
DR HAMAP; MF_01433; Pyrim_hydro_RihB; 1.
DR InterPro; IPR015910; I/U_nuclsd_hydro_CS.
DR InterPro; IPR001910; Inosine/uridine_hydrolase_dom.
DR InterPro; IPR023186; IUNH.
DR InterPro; IPR022977; Pyrim_hydro_RihB.
DR InterPro; IPR036452; Ribo_hydro-like.
DR PANTHER; PTHR12304; PTHR12304; 1.
DR Pfam; PF01156; IU_nuc_hydro; 1.
DR SUPFAM; SSF53590; SSF53590; 1.
DR PROSITE; PS01247; IUNH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Glycosidase; Hydrolase; Metal-binding;
KW Reference proteome.
FT CHAIN 1..313
FT /note="Pyrimidine-specific ribonucleoside hydrolase RihB"
FT /id="PRO_0000206824"
FT ACT_SITE 11
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT BINDING 11
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 16
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 124
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 227
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 239
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 240
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT MUTAGEN 82
FT /note="H->N: Increases KM for uridine 2-fold. Increases
FT kcat 3-fold."
FT /evidence="ECO:0000269|PubMed:15130467"
FT MUTAGEN 239
FT /note="H->A: Increases KM for uridine 13-fold. No effect on
FT kcat."
FT /evidence="ECO:0000269|PubMed:15130467"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 14..25
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 29..36
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 43..56
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 79..82
FT /evidence="ECO:0007829|PDB:1Q8F"
FT TURN 83..85
FT /evidence="ECO:0007829|PDB:3B9X"
FT HELIX 104..114
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 119..123
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 128..136
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 138..143
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 144..150
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 158..162
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 165..168
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 171..178
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 184..187
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 189..192
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 199..208
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 210..231
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 234..237
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 241..248
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 250..252
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 253..258
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:1Q8F"
FT TURN 268..271
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:1Q8F"
FT STRAND 287..293
FT /evidence="ECO:0007829|PDB:1Q8F"
FT HELIX 295..307
FT /evidence="ECO:0007829|PDB:1Q8F"
SQ SEQUENCE 313 AA; 33748 MW; BA3FA8B975474B28 CRC64;
MEKRKIILDC DPGHDDAIAI MMAAKHPAID LLGITIVAGN QTLDKTLING LNVCQKLEIN
VPVYAGMPQP IMRQQIVADN IHGETGLDGP VFEPLTRQAE STHAVKYIID TLMASDGDIT
LVPVGPLSNI AVAMRMQPAI LPKIREIVLM GGAYGTGNFT PSAEFNIFAD PEAARVVFTS
GVPLVMMGLD LTNQTVCTPD VIARMERAGG PAGELFSDIM NFTLKTQFEN YGLAGGPVHD
ATCIGYLINP DGIKTQEMYV EVDVNSGPCY GRTVCDELGV LGKPANTKVG ITIDTDWFWG
LVEECVRGYI KTH
