GPH_ECOLI
ID GPH_ECOLI Reviewed; 252 AA.
AC P32662; Q2M750;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Phosphoglycolate phosphatase;
DE Short=PGP;
DE Short=PGPase;
DE EC=3.1.3.18;
GN Name=gph; Synonyms=yhfE; OrderedLocusNames=b3385, JW3348;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7603433; DOI=10.1007/bf00290345;
RA Lyngstadaas A., Lobner-Olesen A., Boye E.;
RT "Characterization of three genes in the dam-containing operon of
RT Escherichia coli.";
RL Mol. Gen. Genet. 247:546-554(1995).
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 CATALYTIC ACTIVITY.
RX PubMed=10572959; DOI=10.1016/s0304-4165(99)00146-4;
RA Lyngstadaas A., Lobner-Olesen A., Grelland E., Boye E.;
RT "The gene for 2-phosphoglycolate phosphatase (gph) in Escherichia coli is
RT located in the same operon as dam and at least five other diverse genes.";
RL Biochim. Biophys. Acta 1472:376-384(1999).
RN [5]
RP PHYSIOLOGICAL ROLE, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP TRANSCRIPTIONAL REGULATION.
RC STRAIN=K12;
RX PubMed=13129953; DOI=10.1128/jb.185.19.5815-5821.2003;
RA Pellicer M.T., Nunez M.F., Aguilar J., Badia J., Baldoma L.;
RT "Role of 2-phosphoglycolate phosphatase of Escherichia coli in metabolism
RT of the 2-phosphoglycolate formed in DNA repair.";
RL J. Bacteriol. 185:5815-5821(2003).
RN [6]
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).
CC -!- FUNCTION: Specifically catalyzes the dephosphorylation of 2-
CC phosphoglycolate (2P-Gly). Is involved in the dissimilation of the
CC intracellular 2-phosphoglycolate formed during the DNA repair of 3'-
CC phosphoglycolate ends, a major class of DNA lesions induced by
CC oxidative stress. {ECO:0000269|PubMed:16990279}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-phosphoglycolate + H2O = glycolate + phosphate;
CC Xref=Rhea:RHEA:14369, ChEBI:CHEBI:15377, ChEBI:CHEBI:29805,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58033; EC=3.1.3.18;
CC Evidence={ECO:0000269|PubMed:10572959};
CC -!- COFACTOR:
CC Name=chloride; Xref=ChEBI:CHEBI:17996;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=210 uM for 2P-Gly {ECO:0000269|PubMed:13129953,
CC ECO:0000269|PubMed:16990279};
CC KM=8.9 mM for acetyl-phosphate (with magnesium ions as cofactor and
CC at pH 9) {ECO:0000269|PubMed:13129953, ECO:0000269|PubMed:16990279};
CC KM=0.13 mM for imido-diphosphate (with magnesium ions as cofactor and
CC at pH 9) {ECO:0000269|PubMed:13129953, ECO:0000269|PubMed:16990279};
CC Vmax=208 umol/min/mg enzyme {ECO:0000269|PubMed:13129953,
CC ECO:0000269|PubMed:16990279};
CC pH dependence:
CC Optimum pH is 6.9. {ECO:0000269|PubMed:13129953,
CC ECO:0000269|PubMed:16990279};
CC -!- PATHWAY: Organic acid metabolism; glycolate biosynthesis; glycolate
CC from 2-phosphoglycolate: step 1/1.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:13129953}.
CC -!- INDUCTION: Constitutively expressed. {ECO:0000269|PubMed:13129953}.
CC -!- SIMILARITY: Belongs to the HAD-like hydrolase superfamily.
CC CbbY/CbbZ/Gph/YieH family. {ECO:0000305}.
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DR EMBL; Z19601; CAA79664.1; -; Genomic_DNA.
DR EMBL; U18997; AAA58182.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76410.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77906.1; -; Genomic_DNA.
DR PIR; S55288; S55288.
DR RefSeq; NP_417844.1; NC_000913.3.
DR RefSeq; WP_001031729.1; NZ_STEB01000004.1.
DR AlphaFoldDB; P32662; -.
DR SMR; P32662; -.
DR BioGRID; 4259294; 62.
DR BioGRID; 852204; 2.
DR IntAct; P32662; 13.
DR STRING; 511145.b3385; -.
DR SWISS-2DPAGE; P32662; -.
DR jPOST; P32662; -.
DR PaxDb; P32662; -.
DR PRIDE; P32662; -.
DR DNASU; 947895; -.
DR EnsemblBacteria; AAC76410; AAC76410; b3385.
DR EnsemblBacteria; BAE77906; BAE77906; BAE77906.
DR GeneID; 947895; -.
DR KEGG; ecj:JW3348; -.
DR KEGG; eco:b3385; -.
DR PATRIC; fig|1411691.4.peg.3345; -.
DR EchoBASE; EB1817; -.
DR eggNOG; COG0546; Bacteria.
DR HOGENOM; CLU_045011_19_1_6; -.
DR InParanoid; P32662; -.
DR OMA; YLCGKFG; -.
DR PhylomeDB; P32662; -.
DR BioCyc; EcoCyc:GPH-MON; -.
DR BioCyc; MetaCyc:GPH-MON; -.
DR SABIO-RK; P32662; -.
DR UniPathway; UPA00865; UER00834.
DR PRO; PR:P32662; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0031404; F:chloride ion binding; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0008967; F:phosphoglycolate phosphatase activity; IDA:EcoCyc.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0016311; P:dephosphorylation; IDA:EcoCyc.
DR GO; GO:0006281; P:DNA repair; IMP:EcoCyc.
DR GO; GO:0046295; P:glycolate biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 1.10.150.240; -; 1.
DR Gene3D; 3.40.50.1000; -; 1.
DR HAMAP; MF_00495; GPH_hydrolase_bact; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006439; HAD-SF_hydro_IA.
DR InterPro; IPR041492; HAD_2.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR023198; PGP-like_dom2.
DR InterPro; IPR006346; PGPase/MupP.
DR InterPro; IPR037512; PGPase_prok.
DR Pfam; PF13419; HAD_2; 1.
DR PRINTS; PR00413; HADHALOGNASE.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01549; HAD-SF-IA-v1; 1.
DR TIGRFAMs; TIGR01509; HAD-SF-IA-v3; 1.
DR TIGRFAMs; TIGR01449; PGP_bact; 1.
PE 1: Evidence at protein level;
KW Carbohydrate metabolism; Chloride; Hydrolase; Magnesium; Metal-binding;
KW Reference proteome.
FT CHAIN 1..252
FT /note="Phosphoglycolate phosphatase"
FT /id="PRO_0000108027"
FT ACT_SITE 13
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT BINDING 13..15
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 13
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 15
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 192
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
SQ SEQUENCE 252 AA; 27389 MW; FC306F044A1E5521 CRC64;
MNKFEDIRGV AFDLDGTLVD SAPGLAAAVD MALYALELPV AGEERVITWI GNGADVLMER
ALTWARQERA TQRKTMGKPP VDDDIPAEEQ VRILRKLFDR YYGEVAEEGT FLFPHVADTL
GALQAKGLPL GLVTNKPTPF VAPLLEALDI AKYFSVVIGG DDVQNKKPHP DPLLLVAERM
GIAPQQMLFV GDSRNDIQAA KAAGCPSVGL TYGYNYGEAI DLSQPDVIYQ SINDLLPALG
LPHSENQESK ND
