SUPH_ECOLI
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 03-AUG-2022, entry version 161.
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; 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 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 [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}.
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; 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_SSZK01000002.1.
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 PDBsum; 1RLM; -.
DR PDBsum; 1RLO; -.
DR PDBsum; 1RLT; -.
DR PDBsum; 2HF2; -.
DR AlphaFoldDB; P75792; -.
DR SMR; P75792; -.
DR BioGRID; 4262995; 214.
DR IntAct; P75792; 10.
DR STRING; 511145.b0822; -.
DR DrugBank; DB04156; Aspartate beryllium trifluoride.
DR jPOST; P75792; -.
DR PaxDb; P75792; -.
DR PRIDE; P75792; -.
DR DNASU; 945432; -.
DR EnsemblBacteria; AAC73909; AAC73909; b0822.
DR EnsemblBacteria; BAA35503; BAA35503; BAA35503.
DR GeneID; 945432; -.
DR KEGG; ecj:JW0806; -.
DR KEGG; eco:b0822; -.
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 PhylomeDB; P75792; -.
DR BioCyc; EcoCyc:G6425-MON; -.
DR BioCyc; MetaCyc:G6425-MON; -.
DR EvolutionaryTrace; P75792; -.
DR PRO; PR:P75792; -.
DR Proteomes; UP000000318; Chromosome.
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 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 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
