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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
 
 
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