Escherichia coli K-12 substr. MG1655 Enzyme: phosphoglycolate phosphatase

Gene: gph Accession Numbers: EG11871 (EcoCyc), b3385, ECK3372

Synonyms: yhfE, HAD10

Regulation Summary Diagram: ?

Regulation summary diagram for gph

The gph gene encodes a haloacid dehalogenase (HAD)-like phosphatase family enzyme with 2-phosphoglycolate phosphatase activity [Lyngstadaas95, Lyngstadaas99, Kuznetsova06]. 2-phosphoglycolate phosphatase is an enzyme of the Calvin Cycle for assimilation of CO2, and it was thus not clear why it would be found in E. coli [Lyngstadaas95, Lyngstadaas99]. However, 2-phosphoglycolate is formed during repair of DNA strand breaks with 3'-phosphoglycolate ends; such breaks can be caused by radiomimetic drugs like bleomycin [Teresa03]. Gph was shown to be involved in the recovery of glycolate from 2-phosphoglycolate released by the activity of DNA repair enzymes after bleomycin treatment [Teresa03].

Deletion of gph resulted in loss of induction of the glc operon by glycolate after bleomycin treatment [Teresa03]. gph mutants also failed to recover as quickly as wild type after bleomycin treatment [Teresa03]. In a previous study gph deletion mutation had no apparent physiological effect [Lyngstadaas99].

Expression of gph appears to be constitutive [Teresa03].

Gph: "phosphoglycolate phosphatase" [Lyngstadaas95]

Citations: [Yan02, Han06]

Locations: cytosol

Map Position: [3,511,653 <- 3,512,411] (75.69 centisomes, 272°)
Length: 759 bp / 252 aa

Molecular Weight of Polypeptide: 27.389 kD (from nucleotide sequence), 27 kD (experimental) [Teresa03 ]

Unification Links: ASAP:ABE-0011058 , EchoBASE:EB1817 , EcoGene:EG11871 , EcoliWiki:b3385 , ModBase:P32662 , OU-Microarray:b3385 , PortEco:gph , Pride:P32662 , Protein Model Portal:P32662 , RefSeq:NP_417844 , RegulonDB:EG11871 , SMR:P32662 , String:511145.b3385 , UniProt:P32662

Relationship Links: InterPro:IN-FAMILY:IPR006346 , InterPro:IN-FAMILY:IPR006439 , InterPro:IN-FAMILY:IPR023198 , InterPro:IN-FAMILY:IPR023214 , Pfam:IN-FAMILY:PF00702 , Prints:IN-FAMILY:PR00413

In Paralogous Gene Group: 276 (8 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006281 - DNA repair Inferred from experiment [Teresa03]
GO:0016311 - dephosphorylation Inferred from experiment [Teresa03]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0046295 - glycolate biosynthetic process Inferred by computational analysis [UniProtGOA12, GOA01a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Teresa03]
GO:0008967 - phosphoglycolate phosphatase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Teresa03]
GO:0031404 - chloride ion binding Inferred from experiment [Teresa03]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, LopezCampistrou05]

MultiFun Terms: information transfer DNA related DNA repair

Essentiality data for gph knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Curated 02-Oct-2006 by Keseler I , SRI International
Last-Curated ? 14-May-2008 by Johnson A , JCVI

Enzymatic reaction of: phosphoglycolate phosphatase

Synonyms: 2-phosphoglycolate phosphohydrolase, HAD10, 2-phosphoglycolate phosphatase

EC Number:

2-phosphoglycolate + H2O <=> glycolate + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for 2-phosphoglycolate: imidodiphosphate [Kuznetsova06 ] , carbamoyl-phosphate [Kuznetsova06 ] , 4-nitrophenyl phosphate [Kuznetsova06 ] , pyridoxal 5'-phosphate [Kuznetsova06 ] , acetyl phosphate [Kuznetsova06 ] , 3-phospho-D-glycerate [Kuznetsova06 ] , 2-phospho-D-glycerate [Kuznetsova06 ] , phosphoenolpyruvate [Kuznetsova06 ]

Gph has a high substrate specificity [Teresa03, Kuznetsova06], but has some phosphatase activity with other phosphorylated substrates [Kuznetsova06]. Gph also has low β-phosphoglucomutase activity with β-glucose-1-P as substrate [Kuznetsova06].

Cofactors or Prosthetic Groups: Mg2+ [Teresa03], chloride [Teresa03]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Teresa03, BRENDA14]

pH(opt): 6.9 [BRENDA14, Teresa03], 6.9 [Teresa03]

Sequence Features

Protein sequence of phosphoglycolate phosphatase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 13
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Protein-Segment 13 -> 15
UniProt: Substrate; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Active-Site 13
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 15
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 192
UniProt: Magnesium; Non-Experimental Qualifier: by similarity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3385 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11871; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Han06: Han MJ, Lee SY (2006). "The Escherichia coli proteome: past, present, and future prospects." Microbiol Mol Biol Rev 70(2);362-439. PMID: 16760308

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kuznetsova06: Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF (2006). "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family." J Biol Chem 281(47):36149-61. PMID: 16990279

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Lyngstadaas95: Lyngstadaas A, Lobner-Olesen A, Boye E (1995). "Characterization of three genes in the dam-containing operon of Escherichia coli." Mol Gen Genet 1995;247(5);546-54. PMID: 7603433

Lyngstadaas99: Lyngstadaas A, Lobner-Olesen A, Grelland E, Boye E (1999). "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." Biochim Biophys Acta 1472(1-2);376-84. PMID: 10572959

Teresa03: Teresa Pellicer M, Felisa Nunez M, Aguilar J, Badia J, Baldoma L (2003). "Role of 2-phosphoglycolate phosphatase of Escherichia coli in metabolism of the 2-phosphoglycolate formed in DNA repair." J Bacteriol 185(19);5815-21. PMID: 13129953

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Yan02: Yan JX, Devenish AT, Wait R, Stone T, Lewis S, Fowler S (2002). "Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli." Proteomics 2(12);1682-98. PMID: 12469338

Other References Related to Gene Regulation

LobnerOlesen92: Lobner-Olesen A, Boye E, Marinus MG (1992). "Expression of the Escherichia coli dam gene." Mol Microbiol 1992;6(13);1841-51. PMID: 1630320

Wu92: Wu TH, Grelland E, Boye E, Marinus MG (1992). "Identification of a weak promoter for the dam gene of Escherichia coli." Biochim Biophys Acta 1992;1131(1);47-52. PMID: 1581360

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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