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

Gene: umpH Accession Numbers: EG10634 (EcoCyc), b0675, ECK0663

Synonyms: nagD

Regulation Summary Diagram: ?

Regulation summary diagram for umpH

UmpH is a ribonucleoside tri-, di-, and monophosphatase with a preference for purines [Tremblay06]. The enzyme was found to degrade "overflow" UMP nucleotides and is required for optimal growth in response to environmental pyrimidine intermediates [Reaves13]. UMP accumulation to levels above the Km of the enzyme, triggered by environmental conditions or artificially induced by mutations in the normal feedback regulation of the pyrimidine biosynthesis pathway, appear to cause the overflow degradation of UMP by UmpH [Reaves13].

Though UmpH is a member of the nag N-acetylglucosamine utilization operon, it is a fairly general ribonucleotide monophosphatase [Peri90, Tremblay06, Kuznetsova06]. A type IIA member of the HAD protein superfamily, UmpH shows peak activity with UMP, but is also a very effective phosphatase with AMP, GMP and CMP [Koonin94, Tremblay06].

The structure of UmpH has been solved to 1.8 Å resolution [Tremblay06].

A umpH null mutant shows somewhat impaired growth upon addition of orotate, an intermediate in the pyrimidine biosynthesis pathway, to the growth medium. However, growth recovers, and the final culture density is higher than for wild type cells [Reaves13]. Overexpression of umpH induces a stress response, including increased expression of rpoH, and enables improved expression of certain recombinant membrane proteins [Skretas12].

UmpH: "UMP degradation" [Reaves13]

Gene Citations: [Plumbridge89, Plumbridge91, Vogler89a, Rogers88a, Plumbridge91a]

Locations: cytosol

Map Position: [698,797 <- 699,549] (15.06 centisomes, 54°)
Length: 753 bp / 250 aa

Molecular Weight of Polypeptide: 27.163 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002296 , CGSC:36240 , DIP:DIP-6861N , EchoBASE:EB0628 , EcoGene:EG10634 , EcoliWiki:b0675 , ModBase:P0AF24 , OU-Microarray:b0675 , PortEco:nagD , PR:PRO_000023339 , Pride:P0AF24 , Protein Model Portal:P0AF24 , RefSeq:NP_415201 , RegulonDB:EG10634 , SMR:P0AF24 , String:511145.b0675 , Swiss-Model:P0AF24 , UniProt:P0AF24

Relationship Links: InterPro:IN-FAMILY:IPR006357 , InterPro:IN-FAMILY:IPR023214 , InterPro:IN-FAMILY:IPR023215 , PDB:Structure:2C4N , Pfam:IN-FAMILY:PF13344

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Instance reaction of [a nucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] → a nucleoside[periplasmic space] + phosphate[periplasmic space]] (no EC#):
i1: a ribonucleoside 5'-monophosphate + H2O → a ribonucleoside + phosphate (

Instance reactions of [a ribonucleoside 5'-monophosphate + H2O → a ribonucleoside + phosphate] (
i2: CMP + H2O → cytidine + phosphate (

i3: UMP + H2O → uridine + phosphate (

i4: GMP + H2O → guanosine + phosphate (

i5: IMP + H2O → inosine + phosphate (

i6: AMP + H2O → adenosine + phosphate (

Genetic Regulation Schematic: ?

Genetic regulation schematic for umpH

GO Terms:

Biological Process: GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [GOA01, Tremblay06]
GO:0046050 - UMP catabolic process Inferred from experiment [Reaves13]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Tremblay06]
GO:0008253 - 5'-nucleotidase activity Inferred from experiment Inferred by computational analysis [GOA01, Tremblay06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides pyrimidine ribonucleotide biosynthesis

Essentiality data for umpH 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]

Curated 17-Mar-2006 by Shearer A , SRI International
Last-Curated ? 15-Aug-2013 by Keseler I , SRI International

Enzymatic reaction of: UMP phosphatase

Synonyms: HAD23, ribonucleotide monophosphatase

EC Number:

a ribonucleoside 5'-monophosphate + H2O <=> a ribonucleoside + 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 a ribonucleoside 5'-monophosphate: UMP [Tremblay06 ]

In Pathways: adenosine nucleotides degradation II , guanosine nucleotides degradation III

Kinetic Parameters:

Km (μM)

pH(opt): 7 [BRENDA14, Proudfoot04], 8 [BRENDA14, Proudfoot04]

Sequence Features

Protein sequence of UMP phosphatase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 9
UniProt: Magnesium.
Metal-Binding-Site 11
UniProt: Magnesium; via carbonyl oxygen.
Active-Site 11
Protein-Segment 42 -> 43
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Amino-Acid-Site 55
UniProt: Orients the Asp-11 for proton transfer during catalytic turnover; Sequence Annotation Type: site.
Sequence-Conflict 97
[Peri90, UniProt10a]
UniProt: (in Ref. 2; AAC09327);
Amino-Acid-Site 146
UniProt: Confers substrate specificity; Sequence Annotation Type: site.
Amino-Acid-Sites-That-Bind 176
UniProt: Substrate.
Metal-Binding-Site 201
UniProt: Magnesium.
Protein-Segment 202 -> 205
UniProt: Substrate binding; Sequence Annotation Type: region of interest.

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


10/20/97 Gene b0675 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10634; 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

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.

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Koonin94: Koonin EV, Tatusov RL (1994). "Computer analysis of bacterial haloacid dehalogenases defines a large superfamily of hydrolases with diverse specificity. Application of an iterative approach to database search." J Mol Biol 244(1);125-32. PMID: 7966317

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

Peri90: Peri KG, Goldie H, Waygood EB (1990). "Cloning and characterization of the N-acetylglucosamine operon of Escherichia coli." Biochem Cell Biol 68(1);123-37. PMID: 2190615

Plumbridge89: Plumbridge JA (1989). "Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon." Mol Microbiol 1989;3(4);505-15. PMID: 2668691

Plumbridge91: Plumbridge J, Kolb A (1991). "CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli." J Mol Biol 1991;217(4);661-79. PMID: 1848637

Plumbridge91a: Plumbridge JA (1991). "Repression and induction of the nag regulon of Escherichia coli K-12: the roles of nagC and nagA in maintenance of the uninduced state." Mol Microbiol 1991;5(8);2053-62. PMID: 1766379

Proudfoot04: Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kitagawa M, Mori H, Savchenko A, Yakunin AF (2004). "General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG." J Biol Chem 279(52);54687-94. PMID: 15489502

Reaves13: Reaves ML, Young BD, Hosios AM, Xu YF, Rabinowitz JD (2013). "Pyrimidine homeostasis is accomplished by directed overflow metabolism." Nature 500(7461);237-41. PMID: 23903661

Rogers88a: Rogers MJ, Ohgi T, Plumbridge J, Soll D (1988). "Nucleotide sequences of the Escherichia coli nagE and nagB genes: the structural genes for the N-acetylglucosamine transport protein of the bacterial phosphoenolpyruvate: sugar phosphotransferase system and for glucosamine-6-phosphate deaminase." Gene 1988;62(2);197-207. PMID: 3284790

Skretas12: Skretas G, Makino T, Varadarajan N, Pogson M, Georgiou G (2012). "Multi-copy genes that enhance the yield of mammalian G protein-coupled receptors in Escherichia coli." Metab Eng 14(5);591-602. PMID: 22609824

Tremblay06: Tremblay LW, Dunaway-Mariano D, Allen KN (2006). "Structure and activity analyses of Escherichia coli K-12 NagD provide insight into the evolution of biochemical function in the haloalkanoic acid dehalogenase superfamily." Biochemistry 45(4);1183-93. PMID: 16430214

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Vogler89a: Vogler AP, Lengeler JW (1989). "Analysis of the nag regulon from Escherichia coli K12 and Klebsiella pneumoniae and of its regulation." Mol Gen Genet 219(1-2);97-105. PMID: 2693951

Other References Related to Gene Regulation

Plumbridge01: Plumbridge J (2001). "DNA binding sites for the Mlc and NagC proteins: regulation of nagE, encoding the N-acetylglucosamine-specific transporter in Escherichia coli." Nucleic Acids Res 29(2);506-14. PMID: 11139621

Plumbridge93: Plumbridge J, Kolb A (1993). "DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo." Mol Microbiol 10(5);973-81. PMID: 7934873

Plumbridge98b: Plumbridge J, Kolb A (1998). "DNA bending and expression of the divergent nagE-B operons." Nucleic Acids Res 26(5);1254-60. PMID: 9469834

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Wed Sep 2, 2015, biocyc13.