YBHA_ECOLI
ID YBHA_ECOLI Reviewed; 272 AA.
AC P21829;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 3.
DT 03-AUG-2022, entry version 164.
DE RecName: Full=Pyridoxal phosphate phosphatase YbhA;
DE Short=PLP phosphatase;
DE EC=3.1.3.74;
GN Name=ybhA; OrderedLocusNames=b0766, JW0749;
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=7665460; DOI=10.1128/jb.177.17.4851-4856.1995;
RA Maupin-Furlow J.A., Rosentel J.K., Lee J.H., Deppenmeier U., Gunsalus R.P.,
RA Shanmugam K.T.;
RT "Genetic analysis of the modABCD (molybdate transport) operon of
RT Escherichia coli.";
RL J. Bacteriol. 177:4851-4856(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / MC1000 / ATCC 39531;
RX PubMed=8564363; DOI=10.1016/s0944-5013(11)80016-9;
RA Walkenhorst H.M., Hemschemeier S.K., Eichenlaub R.;
RT "Molecular analysis of the molybdate uptake operon, modABCD, of Escherichia
RT coli and modR, a regulatory gene.";
RL Microbiol. Res. 150:347-361(1995).
RN [3]
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 [4]
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 [5]
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 [6]
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 [7]
RP FUNCTION AS A PHOSPHATASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP 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).
CC -!- FUNCTION: Catalyzes the dephosphorylation of pyridoxal-phosphate (PLP).
CC Can also hydrolyze erythrose-4-phosphate (Ery4P) and fructose-1,6-bis-
CC phosphate (Fru1,6bisP). {ECO:0000269|PubMed:15808744,
CC ECO:0000269|PubMed:16990279}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + pyridoxal 5'-phosphate = phosphate + pyridoxal;
CC Xref=Rhea:RHEA:20533, ChEBI:CHEBI:15377, ChEBI:CHEBI:17310,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:597326; EC=3.1.3.74;
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=0.37 mM for PLP (in the presence of magnesium ion as cofactor and
CC at pH 9) {ECO:0000269|PubMed:16990279};
CC KM=1.3 mM for Fru1,6bisP (in the presence of magnesium ion as
CC cofactor 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 -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC CbbY/CbbZ/Gph/YieH family. {ECO:0000305}.
CC -!- CAUTION: This ORF is coded on the other strand of an ORF which has been
CC called modD (by PubMed:7665460 and PubMed:8564363), but which seems to
CC be wrong. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=U07867; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U27192; AAB60177.1; -; Genomic_DNA.
DR EMBL; U07867; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; U00096; AAC73853.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35430.1; -; Genomic_DNA.
DR PIR; F64812; F64812.
DR RefSeq; NP_415287.1; NC_000913.3.
DR RefSeq; WP_001300666.1; NZ_LN832404.1.
DR AlphaFoldDB; P21829; -.
DR SMR; P21829; -.
DR BioGRID; 4261146; 12.
DR IntAct; P21829; 3.
DR STRING; 511145.b0766; -.
DR jPOST; P21829; -.
DR PaxDb; P21829; -.
DR PRIDE; P21829; -.
DR DNASU; 945372; -.
DR EnsemblBacteria; AAC73853; AAC73853; b0766.
DR EnsemblBacteria; BAA35430; BAA35430; BAA35430.
DR GeneID; 945372; -.
DR KEGG; ecj:JW0749; -.
DR KEGG; eco:b0766; -.
DR PATRIC; fig|1411691.4.peg.1512; -.
DR EchoBASE; EB1221; -.
DR eggNOG; COG0561; Bacteria.
DR HOGENOM; CLU_044146_1_0_6; -.
DR InParanoid; P21829; -.
DR OMA; WHPDFTD; -.
DR PhylomeDB; P21829; -.
DR BioCyc; EcoCyc:EG11239-MON; -.
DR BioCyc; MetaCyc:EG11239-MON; -.
DR PRO; PR:P21829; -.
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:0016773; F:phosphotransferase activity, alcohol group as acceptor; IDA:EcoliWiki.
DR GO; GO:0033883; F:pyridoxal phosphatase activity; IDA:EcoCyc.
DR GO; GO:0050308; F:sugar-phosphatase activity; IDA:EcoliWiki.
DR GO; GO:0032361; P:pyridoxal phosphate catabolic process; IMP: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; PS01228; COF_1; 1.
DR PROSITE; PS01229; COF_2; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..272
FT /note="Pyridoxal phosphate phosphatase YbhA"
FT /id="PRO_0000054420"
FT ACT_SITE 9
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 9
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
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 /evidence="ECO:0000250"
FT BINDING 43..44
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 200
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
FT BINDING 223
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 226
FT /ligand="phosphate"
FT /ligand_id="ChEBI:CHEBI:43474"
FT /evidence="ECO:0000250"
SQ SEQUENCE 272 AA; 30201 MW; BB4602AB4D26ACD2 CRC64;
MTTRVIALDL DGTLLTPKKT LLPSSIEALA RAREAGYQLI IVTGRHHVAI HPFYQALALD
TPAICCNGTY LYDYHAKTVL EADPMPVIKA LQLIEMLNEH HIHGLMYVDD AMVYEHPTGH
VIRTSNWAQT LPPEQRPTFT QVASLAETAQ QVNAVWKFAL THDDLPQLQH FGKHVEHELG
LECEWSWHDQ VDIARGGNSK GKRLTKWVEA QGWSMENVVA FGDNFNDISM LEAAGTGVAM
GNADDAVKAR ANIVIGDNTT DSIAQFIYSH LI
