P32662 (GPH_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phosphoglycolate phosphatase
Short name=PGP
Short name=PGPase
EC=3.1.3.18

Gene names

Name:	gph
Synonyms:	yhfE
Ordered Locus Names:	b3385, JW3348

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	252 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Specifically catalyzes the dephosphorylation of 2-phosphoglycolate (2P-Gly). Is involved in the dissimilation of the intracellular 2-phosphoglycolate formed during the DNA repair of 3'-phosphoglycolate ends, a major class of DNA lesions induced by oxidative stress. Ref.6
Catalytic activity	2-phosphoglycolate + H2O = glycolate + phosphate. Ref.4
Cofactor	Chloride. Ref.5 Ref.6 Magnesium. Ref.5 Ref.6
Pathway	Organic acid metabolism; glycolate biosynthesis; glycolate from 2-phosphoglycolate: step 1/1. HAMAP-Rule MF_00495
Subunit structure	Monomer. Ref.5
Induction	Constitutively expressed. Ref.5
Sequence similarities	Belongs to the HAD-like hydrolase superfamily. CbbY/CbbZ/Gph/YieH family.
Biophysicochemical properties	Kinetic parameters: KM=210 µM for 2P-Gly Ref.5 Ref.6 KM=8.9 mM for acetyl-phosphate (with magnesium ions as cofactor and at pH 9) KM=0.13 mM for imido-diphosphate (with magnesium ions as cofactor and at pH 9) Vmax=208 µmol/min/mg enzyme pH dependence: Optimum pH is 6.9.

Ontologies

Keywords
Biological process	Carbohydrate metabolism
Ligand	Chloride Magnesium Metal-binding
Molecular function	Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from mutant phenotype Ref.5. Source: EcoCyc glycolate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway reductive pentose-phosphate cycle Inferred from electronic annotation. Source: HAMAP
Molecular_function	chloride ion binding Inferred from direct assay Ref.5. Source: EcoCyc magnesium ion binding Inferred from direct assay Ref.5. Source: EcoCyc phosphoglycolate phosphatase activity Inferred from direct assay Ref.5. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 252	252	Phosphoglycolate phosphatase HAMAP-Rule MF_00495		PRO_0000108027
Regions
	Region	13 – 15	3	Substrate By similarity
Sites
	Active site	13	1	Nucleophile By similarity
	Metal binding	13	1	Magnesium By similarity
	Metal binding	15	1	Magnesium By similarity
	Metal binding	192	1	Magnesium By similarity

Sequences

	Sequence		Length	Mass (Da)
	P32662 [UniParc]. Last modified October 1, 1993. Version 1. Checksum: FC306F044A1E5521	FASTA	252	27,389
	10 20 30 40 50 60 MNKFEDIRGV AFDLDGTLVD SAPGLAAAVD MALYALELPV AGEERVITWI GNGADVLMER 70 80 90 100 110 120 ALTWARQERA TQRKTMGKPP VDDDIPAEEQ VRILRKLFDR YYGEVAEEGT FLFPHVADTL 130 140 150 160 170 180 GALQAKGLPL GLVTNKPTPF VAPLLEALDI AKYFSVVIGG DDVQNKKPHP DPLLLVAERM 190 200 210 220 230 240 GIAPQQMLFV GDSRNDIQAA KAAGCPSVGL TYGYNYGEAI DLSQPDVIYQ SINDLLPALG 250 LPHSENQESK ND

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of three genes in the dam-containing operon of Escherichia coli." Lyngstadaas A., Lobner-Olesen A., Boye E. Mol. Gen. Genet. 247:546-554(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The gene for 2-phosphoglycolate phosphatase (gph) in Escherichia coli is located in the same operon as dam and at least five other diverse genes." Lyngstadaas A., Lobner-Olesen A., Grelland E., Boye E. Biochim. Biophys. Acta 1472:376-384(1999) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY.
[5]	"Role of 2-phosphoglycolate phosphatase of Escherichia coli in metabolism of the 2-phosphoglycolate formed in DNA repair." Pellicer M.T., Nunez M.F., Aguilar J., Badia J., Baldoma L. J. Bacteriol. 185:5815-5821(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PHYSIOLOGICAL ROLE, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, TRANSCRIPTIONAL REGULATION. Strain: K12.
[6]	"Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family." Kuznetsova E., Proudfoot M., Gonzalez C.F., Brown G., Omelchenko M.V., Borozan I., Carmel L., Wolf Y.I., Mori H., Savchenko A.V., Arrowsmith C.H., Koonin E.V., Edwards A.M., Yakunin A.F. J. Biol. Chem. 281:36149-36161(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A PHOSPHATASE, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, COFACTOR.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	Z19601 Genomic DNA. Translation: CAA79664.1. U18997 Genomic DNA. Translation: AAA58182.1. U00096 Genomic DNA. Translation: AAC76410.1. AP009048 Genomic DNA. Translation: BAE77906.1.
PIR	S55288.
RefSeq	NP_417844.1. NC_000913.2. YP_492047.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P32662.
SMR	P32662. Positions 10-236.
ModBase	Search...
Protein-protein interaction databases
IntAct	P32662. 11 interactions.
STRING	511145.b3385.
2D gel databases
SWISS-2DPAGE	P32662.
Proteomic databases
PaxDb	P32662.
PRIDE	P32662.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC76410; AAC76410; b3385. BAE77906; BAE77906; BAE77906.
GeneID	12930300. 947895.
KEGG	ecj:Y75_p3791. eco:b3385.
PATRIC	32122202. VBIEscCol129921_3478.
Organism-specific databases
EchoBASE	EB1817.
EcoGene	EG11871. gph.
Phylogenomic databases
eggNOG	COG0546.
HOGENOM	HOG000248344.
KO	K01091.
OMA	TRKLWMK.
ProtClustDB	PRK13222.
Enzyme and pathway databases
BioCyc	EcoCyc:GPH-MONOMER. ECOL316407:JW3348-MONOMER. MetaCyc:GPH-MONOMER.
BRENDA	3.1.3.18. 2026.
UniPathway	UPA00865; UER00834.
Gene expression databases
Genevestigator	P32662.
Family and domain databases
Gene3D	1.10.150.240. 1 hit. 3.40.50.1000. 1 hit.
HAMAP	MF_00495. GPH_hydrolase_bact.
InterPro	IPR023214. HAD-like_dom. IPR006439. HAD-SF_hydro_IA_v1. IPR006402. HAD-SF_hydro_IA_v3. IPR005833. Haloacid_DH/epoxide_hydro. IPR006346. PGP_bact. IPR023198. PGP_dom2. [Graphical view]
Pfam	PF00702. Hydrolase. 1 hit. [Graphical view]
PRINTS	PR00413. HADHALOGNASE.
SUPFAM	SSF56784. HAD-like_dom. 1 hit.
TIGRFAMs	TIGR01549. HAD-SF-IA-v1. 1 hit. TIGR01509. HAD-SF-IA-v3. 1 hit. TIGR01449. PGP_bact. 1 hit.
ProtoNet	Search...

Entry information

Entry name

GPH_ECOLI

Accession

Primary (citable) accession number: P32662
Secondary accession number(s): Q2M750

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	October 1, 1993
Last modified:	May 1, 2013
This is version 105 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program