YCSE_BACSU
ID YCSE_BACSU Reviewed; 249 AA.
AC P42962;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 2.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YcsE {ECO:0000305|PubMed:26316208};
DE EC=3.1.3.104 {ECO:0000269|PubMed:26316208};
GN Name=ycsE; OrderedLocusNames=BSU04040;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8574415; DOI=10.1099/13500872-141-12-3241;
RA Akagawa E., Kurita K., Sugawara T., Nakamura K., Kasahara Y., Ogasawara N.,
RA Yamane K.;
RT "Determination of a 17,484 bp nucleotide sequence around the 39 degrees
RT region of the Bacillus subtilis chromosome and similarity analysis of the
RT products of putative ORFs.";
RL Microbiology 141:3241-3245(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=8969502; DOI=10.1099/13500872-142-11-3047;
RA Yamane K., Kumano M., Kurita K.;
RT "The 25 degrees-36 degrees region of the Bacillus subtilis chromosome:
RT determination of the sequence of a 146 kb segment and identification of 113
RT genes.";
RL Microbiology 142:3047-3056(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP SEQUENCE REVISION TO 155-158 AND 181-186.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP PATHWAY, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=26316208; DOI=10.1002/cbic.201500352;
RA Sarge S., Haase I., Illarionov B., Laudert D., Hohmann H.P., Bacher A.,
RA Fischer M.;
RT "Catalysis of an essential step in Vitamin B2 biosynthesis by a consortium
RT of broad spectrum hydrolases.";
RL ChemBioChem 16:2466-2469(2015).
RN [6]
RP FUNCTION, AND COFACTOR.
RX PubMed=25848029; DOI=10.1073/pnas.1423570112;
RA Huang H., Pandya C., Liu C., Al-Obaidi N.F., Wang M., Zheng L.,
RA Toews Keating S., Aono M., Love J.D., Evans B., Seidel R.D.,
RA Hillerich B.S., Garforth S.J., Almo S.C., Mariano P.S., Dunaway-Mariano D.,
RA Allen K.N., Farelli J.D.;
RT "Panoramic view of a superfamily of phosphatases through substrate
RT profiling.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:E1974-E1983(2015).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=27784292; DOI=10.1186/s12866-016-0866-5;
RA Terakawa A., Natsume A., Okada A., Nishihata S., Kuse J., Tanaka K.,
RA Takenaka S., Ishikawa S., Yoshida K.I.;
RT "Bacillus subtilis 5'-nucleotidases with various functions and substrate
RT specificities.";
RL BMC Microbiol. 16:249-249(2016).
CC -!- FUNCTION: Catalyzes the dephosphorylation of the riboflavin precursor
CC 5-amino-6-(5-phospho-D-ribitylamino)uracil and of flavin mononucleotide
CC (FMN) in vitro (PubMed:26316208). To a lesser extent, may also catalyze
CC the dephosphorylation of a broad range of substrates such as
CC phosphorylated sugars and triphosphate nucleotides in vitro
CC (PubMed:26316208, PubMed:25848029). {ECO:0000269|PubMed:25848029,
CC ECO:0000269|PubMed:26316208, ECO:0000269|PubMed:27784292}.
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:26316208};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:25848029, ECO:0000269|PubMed:26316208};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=54 uM for 5-amino-6-(5-phospho-D-ribitylamino)uracil
CC {ECO:0000269|PubMed:26316208};
CC Vmax=12 umol/min/mg enzyme with 5-amino-6-(5-phospho-D-
CC ribitylamino)uracil as substrate {ECO:0000269|PubMed:26316208};
CC Vmax=25 umol/min/mg enzyme with flavin mononucleotide as substrate
CC {ECO:0000269|PubMed:26316208};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 4/4. {ECO:0000269|PubMed:26316208}.
CC -!- DISRUPTION PHENOTYPE: No visible phenotype during normal growth or
CC under oxidative stress caused by diamide.
CC {ECO:0000269|PubMed:27784292}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. Cof family.
CC {ECO:0000305}.
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DR EMBL; D38161; BAA07356.1; -; Genomic_DNA.
DR EMBL; D50453; BAA09035.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12212.2; -; Genomic_DNA.
DR PIR; I39893; I39893.
DR RefSeq; NP_388286.2; NC_000964.3.
DR RefSeq; WP_003234424.1; NZ_JNCM01000031.1.
DR AlphaFoldDB; P42962; -.
DR SMR; P42962; -.
DR STRING; 224308.BSU04040; -.
DR jPOST; P42962; -.
DR PRIDE; P42962; -.
DR EnsemblBacteria; CAB12212; CAB12212; BSU_04040.
DR GeneID; 938252; -.
DR KEGG; bsu:BSU04040; -.
DR PATRIC; fig|224308.179.peg.430; -.
DR eggNOG; COG0561; Bacteria.
DR InParanoid; P42962; -.
DR OMA; WFWAYST; -.
DR PhylomeDB; P42962; -.
DR BioCyc; BSUB:BSU04040-MON; -.
DR BioCyc; MetaCyc:BSU04040-MON; -.
DR BRENDA; 3.1.3.104; 658.
DR SABIO-RK; P42962; -.
DR UniPathway; UPA00275; UER00403.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0043726; F:5-amino-6-(5-phosphoribitylamino)uracil phosphatase activity; IEA:RHEA.
DR GO; GO:0000287; F:magnesium ion binding; IBA:GO_Central.
DR GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.40.50.1000; -; 1.
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; TIGR01484; HAD-SF-IIB; 1.
DR PROSITE; PS01228; COF_1; 1.
DR PROSITE; PS01229; COF_2; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Metal-binding; Reference proteome;
KW Riboflavin biosynthesis.
FT CHAIN 1..249
FT /note="5-amino-6-(5-phospho-D-ribitylamino)uracil
FT phosphatase YcsE"
FT /id="PRO_0000054429"
FT ACT_SITE 16
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 16
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 17
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 18
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 50..51
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 177
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 200
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 201
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 203
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT CONFLICT 155..158
FT /note="NKEL -> TKSS (in Ref. 1; BAA07356 and 2; BAA09035)"
FT /evidence="ECO:0000305"
FT CONFLICT 181..186
FT /note="LAKVTE -> PCQGYG (in Ref. 1; BAA07356 and 2;
FT BAA09035)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 249 AA; 28186 MW; A193E3CDACFF3EF2 CRC64;
MSVQREDVDI KLIAIDMDGT LLNDEQLISD ENRKAIREAE DKGVYVVIST GRTLMTCREL
AESLKLSSFL ITANGSEIWD SNFNLVERKL LHTDHIQMMW DLRNKHNTNF WASTVNKVWR
GEFPENITDH EWLKFGFDIE DDDIRNEVLE ELRKNKELEI TNSSPTNIEV NALGINKAAA
LAKVTEKLGF TMENVMAMGD SLNDIAMIKE AGLGVAMGNA QDIVKETADY ITDTNIEDGV
AKAIRHWVL
