ID   SUPH_ECOLI              Reviewed;         271 AA.
AC   P75792;
DT   30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1997, sequence version 1.
DT   28-JAN-2026, entry version 172.
DE   RecName: Full=Sugar phosphatase YbiV;
DE            EC=3.1.3.23;
GN   Name=ybiV; Synonyms=supH; OrderedLocusNames=b0822, JW0806;
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   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   [5]
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   [6]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH PHOSPHATE ANALOGS AND
RP   MAGNESIUM ION, FUNCTION AS A PHOSPHATASE, CATALYTIC ACTIVITY,
RP   BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=15657928; DOI=10.1002/prot.20267;
RA   Roberts A., Lee S.-Y., McCullagh E., Silversmith R.E., Wemmer D.E.;
RT   "Ybiv from Escherichia coli K12 is a HAD phosphatase.";
RL   Proteins 58:790-801(2005).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 2-271, AND SUBUNIT.
RG   New York structural genomix research consortium (NYSGXRC);
RT   "Domain shifting confirms monomeric structure of Escherichia coli sugar
RT   phosphatase suph.";
RL   Submitted (JUL-2011) to the PDB data bank.
CC   -!- FUNCTION: Catalyzes the hydrolysis of sugar phosphate to sugar and
CC       inorganic phosphate. Has a wide substrate specificity catalyzing the
CC       hydrolysis of ribose-5-phosphate, glucose-6-phosphate, fructose-1-
CC       phosphate, acetyl-phosphate, glycerol-1-phosphate, glycerol-2-
CC       phosphate, 2-deoxy-glucose-6-phosphate, mannose-6-phosphate and
CC       fructose-6-phosphate. Appears to have a low level of phosphotransferase
CC       activity using monophosphates as the phosphate donor.
CC       {ECO:0000269|PubMed:15657928, ECO:0000269|PubMed:15808744,
CC       ECO:0000269|PubMed:16990279}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=sugar phosphate + H2O = sugar + phosphate.; EC=3.1.3.23;
CC         Evidence={ECO:0000269|PubMed:15657928};
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=0.12 mM for imido-di-phosphate (in the presence of magnesium ion
CC         as cofactor and at pH 9) {ECO:0000269|PubMed:15657928,
CC         ECO:0000269|PubMed:16990279};
CC         KM=1.4 mM for fructose-1-phosphate (in the presence of magnesium ion
CC         as cofactor and at pH 9) {ECO:0000269|PubMed:15657928,
CC         ECO:0000269|PubMed:16990279};
CC         KM=2.4 mM for ribose-5-phosphate (in the presence of magnesium ion as
CC         cofactor and at pH 9) {ECO:0000269|PubMed:15657928,
CC         ECO:0000269|PubMed:16990279};
CC         KM=3.1 mM for glucose-6-phosphate (in the presence of magnesium ion
CC         as cofactor and at pH 9) {ECO:0000269|PubMed:15657928,
CC         ECO:0000269|PubMed:16990279};
CC         KM=4.9 mM for acetyl-phosphate (in the presence of magnesium ion as
CC         cofactor and at pH 9) {ECO:0000269|PubMed:15657928,
CC         ECO:0000269|PubMed:16990279};
CC         KM=6 mM for ribose-5-phosphate (at pH 5.4)
CC         {ECO:0000269|PubMed:15657928, ECO:0000269|PubMed:16990279};
CC         KM=6 mM for glycerol-1-phosphate (at pH 5.4)
CC         {ECO:0000269|PubMed:15657928, ECO:0000269|PubMed:16990279};
CC         KM=4.5 mM for glycerol-2-phosphate (at pH 5.4)
CC         {ECO:0000269|PubMed:15657928, ECO:0000269|PubMed:16990279};
CC         Note=Glucose-6-phosphate is also a good substrate with a relative
CC         activity of 62.5% versus the activity with ribose-5-phosphate.;
CC   -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15657928, ECO:0000269|Ref.7}.
CC   -!- INDUCTION: Regulated by the cAMP receptor protein crp. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. Cof family.
CC       SupH subfamily. {ECO:0000305}.
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DR   EMBL; U00096; AAC73909.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA35503.1; -; Genomic_DNA.
DR   PIR; F64819; F64819.
DR   RefSeq; NP_415343.1; NC_000913.3.
DR   RefSeq; WP_000114272.1; NZ_CP009789.1.
DR   PDB; 1RLM; X-ray; 1.90 A; A/B/C/D=1-271.
DR   PDB; 1RLO; X-ray; 2.00 A; A/B/C/D=1-271.
DR   PDB; 1RLT; X-ray; 2.20 A; A/B/C/D=1-271.
DR   PDB; 2HF2; X-ray; 1.90 A; A/B=1-271.
DR   AlphaFoldDB; P75792; -.
DR   SMR; P75792; -.
DR   BioGRID; 4262995; 226.
DR   FunCoup; P75792; 44.
DR   IntAct; P75792; 10.
DR   STRING; 511145.b0822; -.
DR   DrugBank; DB04156; Aspartate beryllium trifluoride.
DR   jPOST; P75792; -.
DR   PaxDb; 511145-b0822; -.
DR   DNASU; 945432; -.
DR   EnsemblBacteria; AAC73909; AAC73909; b0822.
DR   GeneID; 945432; -.
DR   KEGG; ecj:JW0806; -.
DR   KEGG; eco:b0822; -.
DR   KEGG; ecoc:C3026_05165; -.
DR   PATRIC; fig|1411691.4.peg.1456; -.
DR   EchoBASE; EB3111; -.
DR   eggNOG; COG0561; Bacteria.
DR   HOGENOM; CLU_044146_5_0_6; -.
DR   InParanoid; P75792; -.
DR   OMA; VKYAFAM; -.
DR   OrthoDB; 3180855at2; -.
DR   PhylomeDB; P75792; -.
DR   BioCyc; EcoCyc:G6425-MONOMER; -.
DR   BioCyc; MetaCyc:G6425-MONOMER; -.
DR   EvolutionaryTrace; P75792; -.
DR   PRO; PR:P75792; -.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0103026; F:fructose-1-phosphatase activity; IDA:EcoCyc.
DR   GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR   GO; GO:0016791; F:phosphatase activity; IBA:GO_Central.
DR   GO; GO:0050286; F:sorbitol-6-phosphatase activity; IDA:EcoCyc.
DR   GO; GO:0050308; F:sugar-phosphatase activity; IDA:EcoCyc.
DR   CDD; cd07518; HAD_YbiV-Like; 1.
DR   FunFam; 3.30.1240.10:FF:000003; HAD family hydrolase; 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.
DR   PDBsum; 1RLM; -.
DR   PDBsum; 1RLO; -.
DR   PDBsum; 1RLT; -.
DR   PDBsum; 2HF2; -.
PE   1: Evidence at protein level;
KW   3D-structure; Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT   CHAIN           1..271
FT                   /note="Sugar phosphatase YbiV"
FT                   /id="PRO_0000054421"
FT   ACT_SITE        9
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255"
FT   BINDING         9
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         10
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT   BINDING         11
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         44..45
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT   BINDING         192
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT   BINDING         215
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         216
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         218
FT                   /ligand="phosphate"
FT                   /ligand_id="ChEBI:CHEBI:43474"
FT                   /evidence="ECO:0000250"
FT   STRAND          5..8
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           10..14
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           23..36
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          39..43
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           48..51
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           52..54
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   TURN            56..61
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          62..66
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           67..69
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          71..74
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          77..81
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           86..97
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          103..110
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          112..115
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           120..127
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          131..137
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           139..141
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          146..152
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           155..157
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           158..168
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   TURN            169..171
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          172..177
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          182..186
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           192..203
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           207..209
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          210..214
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           217..219
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           220..225
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          227..231
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           237..242
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   STRAND          244..246
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           250..252
FT                   /evidence="ECO:0007829|PDB:1RLM"
FT   HELIX           254..264
FT                   /evidence="ECO:0007829|PDB:1RLM"
SQ   SEQUENCE   271 AA;  30413 MW;  F8733636B422A9A9 CRC64;
     MSVKVIVTDM DGTFLNDAKT YNQPRFMAQY QELKKRGIKF VVASGNQYYQ LISFFPELKD
     EISFVAENGA LVYEHGKQLF HGELTRHESR IVIGELLKDK QLNFVACGLQ SAYVSENAPE
     AFVALMAKHY HRLKPVKDYQ EIDDVLFKFS LNLPDEQIPL VIDKLHVALD GIMKPVTSGF
     GFIDLIIPGL HKANGISRLL KRWDLSPQNV VAIGDSGNDA EMLKMARYSF AMGNAAENIK
     QIARYATDDN NHEGALNVIQ AVLDNTSPFN S
//