|Gene:||gph||Accession Numbers: EG11871 (EcoCyc), b3385, ECK3372|
Synonyms: yhfE, HAD10
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]
|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
In Paralogous Gene Group: 276 (8 members)
|Biological Process:||GO:0006281 - DNA repair
GO:0016311 - dephosphorylation [Teresa03]
GO:0005975 - carbohydrate metabolic process [UniProtGOA11a, GOA06]
GO:0008152 - metabolic process [GOA01a]
GO:0046295 - glycolate biosynthetic process [UniProtGOA12, GOA01a]
|Molecular Function:||GO:0000287 - magnesium ion binding
GO:0008967 - phosphoglycolate phosphatase activity [GOA06, GOA01, GOA01a, Teresa03]
GO:0031404 - chloride ion binding [Teresa03]
GO:0016787 - hydrolase activity [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09, LopezCampistrou05]|
|MultiFun Terms:||information transfer → DNA related → DNA repair|
|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]
Enzymatic reaction of: phosphoglycolate phosphatase
Synonyms: 2-phosphoglycolate phosphohydrolase, HAD10, 2-phosphoglycolate phosphatase
EC Number: 220.127.116.11
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].
|Protein-Segment||13 -> 15|
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
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
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
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
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
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