RIBX_ECOLI
ID RIBX_ECOLI Reviewed; 160 AA.
AC P30176;
DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1993, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=N-glycosidase YbiA {ECO:0000305|PubMed:25431972};
DE EC=3.2.2.- {ECO:0000269|PubMed:25431972};
DE AltName: Full=Riboflavin biosynthesis intermediates N-glycosidase {ECO:0000305|PubMed:25431972};
GN Name=ybiA; OrderedLocusNames=b0798, JW0783;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8037924; DOI=10.1266/jjg.69.1;
RA Ohmori H.;
RT "Structural analysis of the rhlE gene of Escherichia coli.";
RL Jpn. J. Genet. 69:1-12(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
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 [4]
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 [5]
RP FUNCTION IN SWARMING MOTILITY, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=17122336; DOI=10.1128/jb.01294-06;
RA Inoue T., Shingaki R., Hirose S., Waki K., Mori H., Fukui K.;
RT "Genome-wide screening of genes required for swarming motility in
RT Escherichia coli K-12.";
RL J. Bacteriol. 189:950-957(2007).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF GLU-48; TRP-89;
RP ASP-130 AND TRP-133.
RX PubMed=25431972; DOI=10.1042/bj20141237;
RA Frelin O., Huang L., Hasnain G., Jeffryes J.G., Ziemak M.J., Rocca J.R.,
RA Wang B., Rice J., Roje S., Yurgel S.N., Gregory J.F. III, Edison A.S.,
RA Henry C.S., de Crecy-Lagard V., Hanson A.D.;
RT "A directed-overflow and damage-control N-glycosidase in riboflavin
RT biosynthesis.";
RL Biochem. J. 466:137-145(2015).
RN [7]
RP STRUCTURE BY NMR.
RG Northeast structural genomics consortium (NESG);
RT "NMR structure of the E.coli protein ybiA, Northeast structural genomics
RT target ET24.";
RL Submitted (NOV-2005) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the hydrolysis of the N-glycosidic bond in the
CC first two intermediates of riboflavin biosynthesis, which are highly
CC reactive metabolites, yielding relatively innocuous products. Thus, can
CC divert a surplus of harmful intermediates into relatively harmless
CC products and pre-empt the damage these intermediates would otherwise
CC do. Helps maintain flavin levels. May act on other substrates in vivo.
CC Has no activity against GTP, nucleoside monophosphates or ADP-ribose
CC (PubMed:25431972). Is Required for swarming motility (PubMed:17122336).
CC {ECO:0000269|PubMed:17122336, ECO:0000269|PubMed:25431972}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine +
CC H2O = 2,5,6-triamino-4-hydroxypyrimidine + D-ribose 5-phosphate;
CC Xref=Rhea:RHEA:23436, ChEBI:CHEBI:15377, ChEBI:CHEBI:58614,
CC ChEBI:CHEBI:78346, ChEBI:CHEBI:137796;
CC Evidence={ECO:0000269|PubMed:25431972};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-6-(5-phospho-D-ribosylamino)uracil + H2O = 5,6-
CC diaminouracil + D-ribose 5-phosphate; Xref=Rhea:RHEA:55020,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:46252, ChEBI:CHEBI:58453,
CC ChEBI:CHEBI:78346; Evidence={ECO:0000269|PubMed:25431972};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=4.04 mM for 2,5-diamino-6-hydroxy-4-(5-phospho-D-
CC ribosylamino)pyrimidine {ECO:0000269|PubMed:25431972};
CC KM=5.84 mM for 5-amino-6-(5-phospho-D-ribosylamino)uracil
CC {ECO:0000269|PubMed:25431972};
CC Note=kcat is 0.006 sec(-1) with 2,5-diamino-6-hydroxy-4-(5-phospho-D-
CC ribosylamino)pyrimidine as substrate. kcat is 0.80 sec(-1) with 5-
CC amino-6-(5-phospho-D-ribosylamino)uracil as substrate.
CC {ECO:0000269|PubMed:25431972};
CC -!- DISRUPTION PHENOTYPE: Strongly represses cell swarming but no effect on
CC cell swimming (PubMed:17122336). Cells lacking this gene show
CC significantly reduced FAD and FMN levels (both by 13%)
CC (PubMed:25431972). {ECO:0000269|PubMed:17122336,
CC ECO:0000269|PubMed:25431972}.
CC -!- SIMILARITY: Belongs to the YbiA family. {ECO:0000305}.
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DR EMBL; L02123; AAA53654.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73885.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35458.1; -; Genomic_DNA.
DR PIR; F64816; F64816.
DR RefSeq; NP_415319.1; NC_000913.3.
DR RefSeq; WP_001145126.1; NZ_SSZK01000002.1.
DR PDB; 2B3W; NMR; -; A=1-160.
DR PDBsum; 2B3W; -.
DR AlphaFoldDB; P30176; -.
DR BMRB; P30176; -.
DR SMR; P30176; -.
DR BioGRID; 4259963; 15.
DR DIP; DIP-11424N; -.
DR IntAct; P30176; 15.
DR STRING; 511145.b0798; -.
DR PaxDb; P30176; -.
DR PRIDE; P30176; -.
DR EnsemblBacteria; AAC73885; AAC73885; b0798.
DR EnsemblBacteria; BAA35458; BAA35458; BAA35458.
DR GeneID; 945426; -.
DR KEGG; ecj:JW0783; -.
DR KEGG; eco:b0798; -.
DR PATRIC; fig|511145.12.peg.825; -.
DR EchoBASE; EB1539; -.
DR eggNOG; COG3236; Bacteria.
DR HOGENOM; CLU_084247_3_1_6; -.
DR InParanoid; P30176; -.
DR OMA; WMMAAKA; -.
DR PhylomeDB; P30176; -.
DR BioCyc; EcoCyc:EG11579-MON; -.
DR BioCyc; MetaCyc:EG11579-MON; -.
DR EvolutionaryTrace; P30176; -.
DR PRO; PR:P30176; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016799; F:hydrolase activity, hydrolyzing N-glycosyl compounds; IDA:UniProtKB.
DR GO; GO:0071978; P:bacterial-type flagellum-dependent swarming motility; IMP:EcoCyc.
DR GO; GO:1901135; P:carbohydrate derivative metabolic process; IDA:UniProtKB.
DR GO; GO:0034656; P:nucleobase-containing small molecule catabolic process; IDA:EcoCyc.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IMP:EcoCyc.
DR CDD; cd15457; NADAR; 1.
DR Gene3D; 1.10.357.40; -; 1.
DR InterPro; IPR012816; NADAR.
DR InterPro; IPR037238; YbiA-like_sf.
DR Pfam; PF08719; NADAR; 1.
DR SUPFAM; SSF143990; SSF143990; 1.
DR TIGRFAMs; TIGR02464; ribofla_fusion; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Glycosidase; Hydrolase; Reference proteome.
FT CHAIN 1..160
FT /note="N-glycosidase YbiA"
FT /id="PRO_0000168724"
FT MUTAGEN 48
FT /note="E->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:25431972"
FT MUTAGEN 89
FT /note="W->A: Large decrease in enzymatic activity."
FT /evidence="ECO:0000269|PubMed:25431972"
FT MUTAGEN 130
FT /note="D->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:25431972"
FT MUTAGEN 133
FT /note="W->A: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:25431972"
FT STRAND 7..10
FT /evidence="ECO:0007829|PDB:2B3W"
FT STRAND 13..19
FT /evidence="ECO:0007829|PDB:2B3W"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:2B3W"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:2B3W"
FT STRAND 42..46
FT /evidence="ECO:0007829|PDB:2B3W"
FT HELIX 47..55
FT /evidence="ECO:0007829|PDB:2B3W"
FT HELIX 59..67
FT /evidence="ECO:0007829|PDB:2B3W"
FT HELIX 71..78
FT /evidence="ECO:0007829|PDB:2B3W"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:2B3W"
FT HELIX 89..106
FT /evidence="ECO:0007829|PDB:2B3W"
FT HELIX 109..117
FT /evidence="ECO:0007829|PDB:2B3W"
FT TURN 118..120
FT /evidence="ECO:0007829|PDB:2B3W"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:2B3W"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:2B3W"
FT TURN 136..139
FT /evidence="ECO:0007829|PDB:2B3W"
FT HELIX 144..160
FT /evidence="ECO:0007829|PDB:2B3W"
SQ SEQUENCE 160 AA; 18669 MW; 28D6DA5C6748653C CRC64;
MPVRAQRIQH VMQDTIINFY STSDDYGDFS NFAAWPIKVD GKTWPTSEHY FQAQKFLDEK
YREEIRRVSS PMVAARMGRD RSKPLRKNWE SVKEQVMRKA LRAKFEQHAE LRALLLATAP
AKLVEHTEND AYWGDGGHGK GKNRLGYLLM ELREQLAIEK