ID   YBJI_ECOLI              Reviewed;         271 AA.
AC   P75809;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   30-MAY-2000, sequence version 3.
DT   28-JAN-2026, entry version 163.
DE   RecName: Full=5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI {ECO:0000303|PubMed:24123841};
DE            EC=3.1.3.104 {ECO:0000269|PubMed:24123841};
GN   Name=ybjI; OrderedLocusNames=b0844, JW5113;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC   Enterobacterales; Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
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   [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   IDENTIFICATION BY MASS SPECTROMETRY.
RC   STRAIN=B / BL21;
RX   PubMed=10493123;
RX   DOI=10.1002/(sici)1522-2683(19990801)20:11<2181::aid-elps2181>3.0.co;2-q;
RA   Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.;
RT   "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite
RT   chromatography.";
RL   Electrophoresis 20:2181-2195(1999).
RN   [5]
RP   FUNCTION AS A PHOSPHATASE.
RX   PubMed=15808744; DOI=10.1016/j.femsre.2004.12.006;
RA   Kuznetsova E., Proudfoot M., Sanders S.A., Reinking J., Savchenko A.,
RA   Arrowsmith C.H., Edwards A.M., Yakunin A.F.;
RT   "Enzyme genomics: application of general enzymatic screens to discover new
RT   enzymes.";
RL   FEMS Microbiol. Rev. 29:263-279(2005).
RN   [6]
RP   FUNCTION AS A PHOSPHATASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP   SPECIFICITY, AND COFACTOR.
RX   PubMed=16990279; DOI=10.1074/jbc.m605449200;
RA   Kuznetsova E., Proudfoot M., Gonzalez C.F., Brown G., Omelchenko M.V.,
RA   Borozan I., Carmel L., Wolf Y.I., Mori H., Savchenko A.V., Arrowsmith C.H.,
RA   Koonin E.V., Edwards A.M., Yakunin A.F.;
RT   "Genome-wide analysis of substrate specificities of the Escherichia coli
RT   haloacid dehalogenase-like phosphatase family.";
RL   J. Biol. Chem. 281:36149-36161(2006).
RN   [7]
RP   FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP   SPECIFICITY, PATHWAY, AND DISRUPTION PHENOTYPE.
RX   PubMed=24123841; DOI=10.1002/cbic.201300544;
RA   Haase I., Sarge S., Illarionov B., Laudert D., Hohmann H.P., Bacher A.,
RA   Fischer M.;
RT   "Enzymes from the haloacid dehalogenase (HAD) superfamily catalyse the
RT   elusive dephosphorylation step of riboflavin biosynthesis.";
RL   ChemBioChem 14:2272-2275(2013).
CC   -!- FUNCTION: Catalyzes the dephosphorylation of 5-amino-6-(5-phospho-D-
CC       ribitylamino)uracil, and thus could be involved in the riboflavin
CC       biosynthesis pathway (PubMed:24123841). Is also able to dephosphorylate
CC       flavin mononucleotide (FMN), erythrose 4-phosphate and other phosphoric
CC       acid esters (PubMed:15808744, PubMed:16990279, PubMed:24123841).
CC       {ECO:0000269|PubMed:15808744, ECO:0000269|PubMed:16990279,
CC       ECO:0000269|PubMed:24123841}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=5-amino-6-(5-phospho-D-ribitylamino)uracil + H2O = 5-amino-6-
CC         (D-ribitylamino)uracil + phosphate; Xref=Rhea:RHEA:25197,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15934, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58421; EC=3.1.3.104;
CC         Evidence={ECO:0000269|PubMed:24123841};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000269|PubMed:16990279};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000269|PubMed:16990279};
CC       Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC         Evidence={ECO:0000269|PubMed:16990279};
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000269|PubMed:16990279};
CC       Note=Magnesium. Can also use other divalent metal cations as manganese,
CC       cobalt or zinc. {ECO:0000269|PubMed:16990279};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=70 uM for 5-amino-6-(5-phospho-D-ribitylamino)uracil
CC         {ECO:0000269|PubMed:24123841};
CC         KM=2.3 mM for FMN (in the presence of magnesium ion as cofactor and
CC         at pH 9) {ECO:0000269|PubMed:16990279};
CC         KM=2.6 mM for Ery4P (in the presence of magnesium ion as cofactor and
CC         at pH 9) {ECO:0000269|PubMed:16990279};
CC         Vmax=3 umol/min/mg enzyme with
CC         5-amino-6-(5-phospho-D-ribitylamino)uracil as substrate
CC         {ECO:0000269|PubMed:24123841};
CC       pH dependence:
CC         Optimum pH is 6-7.5. {ECO:0000269|PubMed:16990279};
CC   -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC       ribitylamino)uracil from GTP: step 4/4. {ECO:0000305|PubMed:24123841}.
CC   -!- DISRUPTION PHENOTYPE: Cells lacking this gene can grow in the absence
CC       of exogenous riboflavin; this may be due to the presence of the
CC       functionally redundant protein YigB. {ECO:0000269|PubMed:24123841}.
CC   -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. Cof family.
CC       {ECO:0000305}.
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DR   EMBL; U00096; AAC73931.2; -; Genomic_DNA.
DR   EMBL; AP009048; BAA35548.2; -; Genomic_DNA.
DR   PIR; D64822; D64822.
DR   RefSeq; NP_415365.4; NC_000913.3.
DR   RefSeq; WP_000023565.1; NZ_CP009789.1.
DR   AlphaFoldDB; P75809; -.
DR   SMR; P75809; -.
DR   BioGRID; 4262830; 128.
DR   FunCoup; P75809; 183.
DR   STRING; 511145.b0844; -.
DR   jPOST; P75809; -.
DR   PaxDb; 511145-b0844; -.
DR   DNASU; 945470; -.
DR   EnsemblBacteria; AAC73931; AAC73931; b0844.
DR   GeneID; 945470; -.
DR   KEGG; ecj:JW5113; -.
DR   KEGG; eco:b0844; -.
DR   KEGG; ecoc:C3026_05275; -.
DR   PATRIC; fig|1411691.4.peg.1434; -.
DR   EchoBASE; EB3442; -.
DR   eggNOG; COG0561; Bacteria.
DR   HOGENOM; CLU_044146_5_0_6; -.
DR   InParanoid; P75809; -.
DR   OMA; PHNNEEG; -.
DR   OrthoDB; 3180855at2; -.
DR   PhylomeDB; P75809; -.
DR   BioCyc; EcoCyc:G6442-MONOMER; -.
DR   BioCyc; MetaCyc:G6442-MONOMER; -.
DR   UniPathway; UPA00275; UER00403.
DR   PRO; PR:P75809; -.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0043726; F:5-amino-6-(5-phosphoribitylamino)uracil phosphatase activity; IDA:EcoCyc.
DR   GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR   GO; GO:0016791; F:phosphatase activity; IDA:UniProtKB.
DR   GO; GO:0009231; P:riboflavin biosynthetic process; IDA:EcoCyc.
DR   CDD; cd07518; HAD_YbiV-Like; 1.
DR   FunFam; 3.30.1240.10:FF:000010; 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YbjI; 1.
DR   Gene3D; 3.30.1240.10; -; 1.
DR   Gene3D; 3.40.50.1000; HAD superfamily/HAD-like; 1.
DR   InterPro; IPR000150; Cof.
DR   InterPro; IPR036412; HAD-like_sf.
DR   InterPro; IPR006379; HAD-SF_hydro_IIB.
DR   InterPro; IPR023214; HAD_sf.
DR   NCBIfam; TIGR00099; Cof-subfamily; 1.
DR   NCBIfam; TIGR01484; HAD-SF-IIB; 1.
DR   PANTHER; PTHR10000:SF53; 5-AMINO-6-(5-PHOSPHO-D-RIBITYLAMINO)URACIL PHOSPHATASE YBJI-RELATED; 1.
DR   PANTHER; PTHR10000; PHOSPHOSERINE PHOSPHATASE; 1.
DR   Pfam; PF08282; Hydrolase_3; 1.
DR   SFLD; SFLDG01144; C2.B.4:_PGP_Like; 1.
DR   SFLD; SFLDG01140; C2.B:_Phosphomannomutase_and_P; 1.
DR   SFLD; SFLDS00003; Haloacid_Dehalogenase; 1.
DR   SUPFAM; SSF56784; HAD-like; 1.
DR   PROSITE; PS01229; COF_2; 1.
PE   1: Evidence at protein level;
KW   Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT   CHAIN           1..271
FT                   /note="5-amino-6-(5-phospho-D-ribitylamino)uracil
FT                   phosphatase YbjI"
FT                   /id="PRO_0000054422"
FT   ACT_SITE        9
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250"
FT   BINDING         9
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         10
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /evidence="ECO:0000250"
FT   BINDING         11
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         44..45
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /evidence="ECO:0000250"
FT   BINDING         192
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /evidence="ECO:0000250"
FT   BINDING         215
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000250"
FT   BINDING         218
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   271 AA;  30196 MW;  AF44E565BCB68BA9 CRC64;
     MSIKLIAVDM DGTFLSDQKT YNRERFMAQY QQMKAQGIRF VVASGNQYYQ LISFFPEIAN
     EIAFVAENGG WVVSEGKDVF NGELSKDAFA TVVEHLLTRP EVEIIACGKN SAYTLKKYDD
     AMKTVAEMYY HRLEYVDNFD NLEDIFFKFG LNLSDELIPQ VQKALHEAIG DIMVSVHTGN
     GSIDLIIPGV HKANGLRQLQ KLWGIDDSEV VVFGDGGNDI EMLRQAGFSF AMENAGSAVV
     AAAKYRAGSN NREGVLDVID KVLKHEAPFD Q
//