YIDA_ECOLI
ID YIDA_ECOLI Reviewed; 270 AA.
AC P0A8Y5; P09997; P76737; Q2M809;
DT 21-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 21-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Sugar phosphatase YidA;
DE EC=3.1.3.23;
GN Name=yidA; OrderedLocusNames=b3697, JW3674;
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 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-195.
RX PubMed=3029692; DOI=10.1093/nar/15.2.771;
RA Adachi T., Mizuuchi M., Robinson E.A., Appella E., O'Dea M.H., Gellert M.,
RA Mizuuchi K.;
RT "DNA sequence of the E. coli gyrB gene: application of a new sequencing
RT strategy.";
RL Nucleic Acids Res. 15:771-784(1987).
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, CATALYTIC ACTIVITY, ACTIVE SITE, MUTAGENESIS OF
RP ASP-9, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE 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 X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 2-270 IN COMPLEX WITH MAGNESIUM
RP IONS, AND SUBUNIT.
RA Ramagopal U.A., Almo S.C.;
RT "Crystal structure of NYSGRC target T1436: a hypothetical protein YidA.";
RL Submitted (MAR-2004) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the dephosphorylation of different sugar phosphates
CC including erythrose-4-phosphate (Ery4P), ribose-5-phosphate (Ribu5P),
CC fructose-1-phosphate (Fru1P), fructose-6-phosphate (Fru6P), glucose-6-P
CC (Glu6P), and also imidodiphosphate (Imido-di-P) and acetyl phosphate
CC (Acetyl-P). Selectively hydrolyzes alpha-D-glucose-1-phosphate (Glu1P)
CC and has no activity with the beta form. {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:16990279};
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=0.019 mM for Ery4P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=0.033 mM for Imido-di-P (in the presence of magnesium ion as
CC cofactor and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=0.21 mM for Glu1P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=0.39 mM for Fru1P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=0.44 mM for Fru6P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=0.45 mM for Ribu5P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=0.54 mM for Man1P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=0.81 mM for Glu6P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=3.8 mM for Acetyl-P (in the presence of magnesium ion as cofactor
CC and at pH 9) {ECO:0000269|PubMed:16990279};
CC pH dependence:
CC Optimum pH is between 6 and 7.5. {ECO:0000269|PubMed:16990279};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|Ref.7}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily. Cof family.
CC {ECO:0000305}.
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DR EMBL; L10328; AAA62048.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76720.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77597.1; -; Genomic_DNA.
DR EMBL; X04341; CAA27873.1; -; Genomic_DNA.
DR PIR; B65172; QQECGB.
DR RefSeq; NP_418152.1; NC_000913.3.
DR RefSeq; WP_000985549.1; NZ_STEB01000015.1.
DR PDB; 1RKQ; X-ray; 1.40 A; A/B=2-270.
DR PDBsum; 1RKQ; -.
DR AlphaFoldDB; P0A8Y5; -.
DR SMR; P0A8Y5; -.
DR BioGRID; 4262577; 36.
DR BioGRID; 852509; 1.
DR DIP; DIP-36033N; -.
DR IntAct; P0A8Y5; 11.
DR STRING; 511145.b3697; -.
DR jPOST; P0A8Y5; -.
DR PaxDb; P0A8Y5; -.
DR PRIDE; P0A8Y5; -.
DR DNASU; 948204; -.
DR EnsemblBacteria; AAC76720; AAC76720; b3697.
DR EnsemblBacteria; BAE77597; BAE77597; BAE77597.
DR GeneID; 66672405; -.
DR GeneID; 948204; -.
DR KEGG; ecj:JW3674; -.
DR KEGG; eco:b3697; -.
DR PATRIC; fig|1411691.4.peg.3006; -.
DR EchoBASE; EB1181; -.
DR eggNOG; COG0561; Bacteria.
DR HOGENOM; CLU_044146_0_1_6; -.
DR InParanoid; P0A8Y5; -.
DR OMA; GAWIQDP; -.
DR PhylomeDB; P0A8Y5; -.
DR BioCyc; EcoCyc:EG11195-MON; -.
DR BioCyc; MetaCyc:EG11195-MON; -.
DR EvolutionaryTrace; P0A8Y5; -.
DR PRO; PR:P0A8Y5; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoliWiki.
DR GO; GO:0016791; F:phosphatase activity; IDA:EcoliWiki.
DR GO; GO:0050308; F:sugar-phosphatase activity; IDA:EcoliWiki.
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; PS01228; COF_1; 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..270
FT /note="Sugar phosphatase YidA"
FT /id="PRO_0000054423"
FT ACT_SITE 9
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:16990279"
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 /evidence="ECO:0000250"
FT BINDING 11
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 43..44
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 197
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 220
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 223
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT MUTAGEN 9
FT /note="D->A: Loss of the phosphatase activity."
FT /evidence="ECO:0000269|PubMed:16990279"
FT STRAND 5..8
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 10..14
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 23..34
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 38..42
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 51..56
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 65..68
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 69..71
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:1RKQ"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 90..103
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 106..110
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 115..117
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 124..132
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 153..157
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 160..169
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 172..177
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 178..184
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 187..192
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 197..208
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 222..224
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 225..230
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 242..247
FT /evidence="ECO:0007829|PDB:1RKQ"
FT STRAND 249..251
FT /evidence="ECO:0007829|PDB:1RKQ"
FT TURN 255..258
FT /evidence="ECO:0007829|PDB:1RKQ"
FT HELIX 259..267
FT /evidence="ECO:0007829|PDB:1RKQ"
SQ SEQUENCE 270 AA; 29721 MW; 04E749788D8A9446 CRC64;
MAIKLIAIDM DGTLLLPDHT ISPAVKNAIA AARARGVNVV LTTGRPYAGV HNYLKELHME
QPGDYCITYN GALVQKAADG STVAQTALSY DDYRFLEKLS REVGSHFHAL DRTTLYTANR
DISYYTVHES FVATIPLVFC EAEKMDPNTQ FLKVMMIDEP AILDQAIARI PQEVKEKYTV
LKSAPYFLEI LDKRVNKGTG VKSLADVLGI KPEEIMAIGD QENDIAMIEY AGVGVAMDNA
IPSVKEVANF VTKSNLEDGV AFAIEKYVLN
