YIGB_ECOLI
ID YIGB_ECOLI Reviewed; 238 AA.
AC P0ADP0; P23306; P76757; Q2M8B8;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB {ECO:0000303|PubMed:24123841};
DE EC=3.1.3.104 {ECO:0000269|PubMed:24123841};
GN Name=yigB; OrderedLocusNames=b3812, JW3785;
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;
RX PubMed=2254268; DOI=10.1128/jb.172.12.6973-6980.1990;
RA Colloms S.D., Sykora P., Szatmari G., Sherratt D.J.;
RT "Recombination at ColE1 cer requires the Escherichia coli xerC gene
RT product, a member of the lambda integrase family of site-specific
RT recombinases.";
RL J. Bacteriol. 172:6973-6980(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1379743; DOI=10.1126/science.1379743;
RA Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.;
RT "Analysis of the Escherichia coli genome: DNA sequence of the region from
RT 84.5 to 86.5 minutes.";
RL Science 257:771-778(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION TO 13.
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 183-238.
RX PubMed=6379604; DOI=10.1093/nar/12.14.5789;
RA Finch P.W., Emmerson P.T.;
RT "The nucleotide sequence of the uvrD gene of E. coli.";
RL Nucleic Acids Res. 12:5789-5799(1984).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 183-238.
RX PubMed=6324092; DOI=10.1093/nar/11.24.8625;
RA Easton A.M., Kushner S.R.;
RT "Transcription of the uvrD gene of Escherichia coli is controlled by the
RT lexA repressor and by attenuation.";
RL Nucleic Acids Res. 11:8625-8640(1983).
RN [7]
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 [8]
RP FUNCTION IN THE FORMATION OF DORMANT PERSISTER CELLS.
RX PubMed=18519731; DOI=10.1128/aac.00144-08;
RA Hansen S., Lewis K., Vulic M.;
RT "Role of global regulators and nucleotide metabolism in antibiotic
RT tolerance in Escherichia coli.";
RL Antimicrob. Agents Chemother. 52:2718-2726(2008).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, DISRUPTION PHENOTYPE, AND PATHWAY.
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) and other phosphoric acid esters
CC (PubMed:16990279) (PubMed:24123841). YigB is important for the
CC formation of dormant persister cells (PubMed:18519731).
CC {ECO:0000269|PubMed:16990279, ECO:0000269|PubMed:18519731,
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=20 uM for 5-amino-6-(5-phospho-D-ribitylamino)uracil
CC {ECO:0000269|PubMed:24123841};
CC KM=1 mM for FMN (with magnesium ions as cofactor and at pH 9)
CC {ECO:0000269|PubMed:16990279};
CC Vmax=4 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 YbjI. {ECO:0000269|PubMed:24123841}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC {ECO:0000305}.
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DR EMBL; M38257; AAA24764.1; -; Genomic_DNA.
DR EMBL; M87049; AAA67608.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76815.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77488.1; -; Genomic_DNA.
DR EMBL; X00738; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; D37841; D37841.
DR RefSeq; NP_418257.1; NC_000913.3.
DR RefSeq; WP_001213584.1; NZ_STEB01000021.1.
DR AlphaFoldDB; P0ADP0; -.
DR SMR; P0ADP0; -.
DR BioGRID; 4263283; 15.
DR DIP; DIP-48086N; -.
DR IntAct; P0ADP0; 1.
DR STRING; 511145.b3812; -.
DR jPOST; P0ADP0; -.
DR PaxDb; P0ADP0; -.
DR PRIDE; P0ADP0; -.
DR DNASU; 948357; -.
DR EnsemblBacteria; AAC76815; AAC76815; b3812.
DR EnsemblBacteria; BAE77488; BAE77488; BAE77488.
DR GeneID; 67414402; -.
DR GeneID; 948357; -.
DR KEGG; ecj:JW3785; -.
DR KEGG; eco:b3812; -.
DR PATRIC; fig|1411691.4.peg.2895; -.
DR EchoBASE; EB1187; -.
DR eggNOG; COG1011; Bacteria.
DR HOGENOM; CLU_045011_8_2_6; -.
DR InParanoid; P0ADP0; -.
DR OMA; PQETHDT; -.
DR PhylomeDB; P0ADP0; -.
DR BioCyc; EcoCyc:EG11202-MON; -.
DR BioCyc; MetaCyc:EG11202-MON; -.
DR UniPathway; UPA00275; UER00403.
DR PRO; PR:P0ADP0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
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:EcoCyc.
DR GO; GO:0016311; P:dephosphorylation; IBA:GO_Central.
DR GO; GO:0022611; P:dormancy process; IMP:EcoCyc.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IDA:EcoCyc.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR Pfam; PF13419; HAD_2; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01549; HAD-SF-IA-v1; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..238
FT /note="5-amino-6-(5-phospho-D-ribitylamino)uracil
FT phosphatase YigB"
FT /id="PRO_0000169651"
FT ACT_SITE 16
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 16..18
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 16
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 18
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 188
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT CONFLICT 13
FT /note="L -> V (in Ref. 2; AAA67608)"
FT /evidence="ECO:0000305"
FT CONFLICT 200
FT /note="S -> T (in Ref. 1; AAA24764)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 238 AA; 27122 MW; 9C1BDE710641E0D6 CRC64;
MRFYRPLGRI SALTFDLDDT LYDNRPVILR TEREALTFVQ NYHPALRSFQ NEDLQRLRQA
VREAEPEIYH DVTRWRFRSI EQAMLDAGLS AEEASAGAHA AMINFAKWRS RIDVPQQTHD
TLKQLAKKWP LVAITNGNAQ PELFGLGDYF EFVLRAGPHG RSKPFSDMYF LAAEKLNVPI
GEILHVGDDL TTDVGGAIRS GMQACWIRPE NGDLMQTWDS RLLPHLEISR LASLTSLI
