YBJI_ECOLI
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 03-AUG-2022, entry version 151.
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; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC 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.fmrre.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 5-amino-6-(5-phospho-D-
CC ribitylamino)uracil as substrate {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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
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_SSUW01000010.1.
DR AlphaFoldDB; P75809; -.
DR SMR; P75809; -.
DR BioGRID; 4262830; 126.
DR STRING; 511145.b0844; -.
DR jPOST; P75809; -.
DR PaxDb; P75809; -.
DR PRIDE; P75809; -.
DR DNASU; 945470; -.
DR EnsemblBacteria; AAC73931; AAC73931; b0844.
DR EnsemblBacteria; BAA35548; BAA35548; BAA35548.
DR GeneID; 945470; -.
DR KEGG; ecj:JW5113; -.
DR KEGG; eco:b0844; -.
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; APHNNEE; -.
DR PhylomeDB; P75809; -.
DR BioCyc; EcoCyc:G6442-MON; -.
DR BioCyc; MetaCyc:G6442-MON; -.
DR UniPathway; UPA00275; UER00403.
DR PRO; PR:P75809; -.
DR Proteomes; UP000000318; Chromosome.
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 Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR000150; Cof.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006379; HAD-SF_hydro_IIB.
DR InterPro; IPR023214; HAD_sf.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR00099; Cof-subfamily; 1.
DR TIGRFAMs; TIGR01484; HAD-SF-IIB; 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
