Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: ADP-sugar pyrophosphatase



Gene: nudF Accession Numbers: EG12633 (EcoCyc), b3034, ECK3025

Synonyms: trgB, aspP, yqiE

Regulation Summary Diagram: ?

Subunit composition of ADP-sugar pyrophosphatase = [NudF]2
         ADP- sugar pyrophosphatase = NudF

Summary:
ADP-glucose is a precursor molecule for glycogen biosynthesis. Overexpression of aspP leads to a reduced amount of glycogen in the cell. AspP is a member of the family of Nudix hydrolases [Bessman96] and has ADP- sugar pyrophosphatase activity [MorenoBruna01]. It is thought to control the flow of carbon toward glycogen, interconnecting gluconeogenesis with other metabolic pathways [MorenoBruna01].

Gel filtration experiments indicate that the enzyme is a dimer in solution [MorenoBruna01]. Crystal structures of AspP in various forms have been solved, showing a domain-swapped dimer where the Nudix motif residues compose a catalytic center [Gabelli01, Badger05]. Further studies suggested the function of the Mg2+ ion and a possible reaction mechanism [Gabelli02].

An E. coli enzyme with a similar catalytic activity has been purified and was thought to be localized in the periplasm [Melo66].

There is no effect on cell growth of either an aspP null mutation or aspP overexpression [MorenoBruna01]. Transcription of aspP is induced by the CreBC two-component system by minimal media growth conditions [Avison01].

aspP shows differential codon adaptation, resulting in differential translation efficiency signatures, in thermophilic microbes. It was therefore predicted to play a role in the heat shock response. An aspP deletion mutant was shown to be more sensitive than wild-type specifically to heat shock, but not other stresses [Krisko14].

Locations: cytosol

Map Position: [3,175,303 <- 3,175,932] (68.44 centisomes)
Length: 630 bp / 209 aa

Molecular Weight of Polypeptide: 23.667 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009961 , DIP:DIP-36214N , EchoBASE:EB2101 , EcoGene:EG12633 , EcoliWiki:b3034 , ModBase:Q93K97 , OU-Microarray:b3034 , PortEco:nudF , PR:PRO_000023424 , Protein Model Portal:Q93K97 , RefSeq:NP_417506 , RegulonDB:EG12633 , SMR:Q93K97 , String:511145.b3034 , UniProt:Q93K97

Relationship Links: InterPro:IN-FAMILY:IPR000086 , InterPro:IN-FAMILY:IPR004385 , InterPro:IN-FAMILY:IPR015797 , InterPro:IN-FAMILY:IPR020084 , PDB:Structure:1G0S , PDB:Structure:1G9Q , PDB:Structure:1GA7 , PDB:Structure:1KHZ , PDB:Structure:1VIQ , Pfam:IN-FAMILY:PF00293 , Prosite:IN-FAMILY:PS00893 , Prosite:IN-FAMILY:PS51462

In Paralogous Gene Group: 481 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Dunn99, UniProtGOA11a, GOA01, GOA01a]
GO:0009408 - response to heat Inferred from experiment [Krisko14]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Dunn99]
GO:0047631 - ADP-ribose diphosphatase activity Inferred from experiment Inferred by computational analysis [GOA01, Dunn99]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, Lasserre06]

MultiFun Terms: cell processes protection
metabolism

Essentiality data for nudF 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]

Enzymatic reaction of: ADP-ribose pyrophosphatase (ADP-sugar pyrophosphatase)

EC Number: 3.6.1.53

ADP-D-ribose + H2O <=> AMP + D-ribofuranose 5-phosphate + 2 H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Cofactors or Prosthetic Groups: Mg2+ [Dunn99]

Kinetic Parameters:

Substrate
Km (μM)
Citations
ADP-D-ribose
67.0
[Dunn99]


Enzymatic reaction of: ADP-sugar pyrophosphatase

Synonyms: ASPPase

EC Number: 3.6.1.21

an ADP-sugar + H2O <=> AMP + an α-D-aldose 1-phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for an ADP-sugar: ADP-D-ribose [MorenoBruna01 ] , ADP-mannose [MorenoBruna01 ] , ADP-α-D-glucose [MorenoBruna01 ]

Summary:
The enzyme is inhibited by phosphorylated compounds such as AMP, ADP, ATP, 3-phosphoglycerate and pyrophosphate [MorenoBruna01].

Inhibitors (Unknown Mechanism): AMP [MorenoBruna01] , ADP [MorenoBruna01] , ATP [MorenoBruna01]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 2
[MorenoBruna01, UniProt10]
Alternate sequence: L → V; UniProt: (in Ref. 1; CAC44036);
Sequence-Conflict 6
[MorenoBruna01, UniProt10]
Alternate sequence: N → S; UniProt: (in Ref. 1; CAC44036);
Protein-Segment 28 -> 29
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Protein-Segment 51 -> 52
[UniProt10]
UniProt: Substrate binding; shared with dimeric partner; Sequence Annotation Type: region of interest;
Conserved-Region 55 -> 193
[UniProt09]
UniProt: Nudix hydrolase;
Amino-Acid-Sites-That-Bind 56
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 79
[UniProt10]
UniProt: Substrate;
Metal-Binding-Site 96
[UniProt10]
UniProt: Magnesium 1; via carbonyl oxygen;
Protein-Segment 97 -> 118
[UniProt10]
UniProt: Nudix box; Sequence Annotation Type: short sequence motif;
Amino-Acid-Sites-That-Bind 98
[UniProt10]
UniProt: Substrate; via amide nitrogen;
Metal-Binding-Site 112
[UniProt10]
UniProt: Magnesium 2;
Metal-Binding-Site 116
[UniProt10]
UniProt: Magnesium 1;
Protein-Segment 133 -> 135
[UniProt10]
UniProt: Substrate binding; shared with dimeric partner; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 139
[UniProt10]
UniProt: Substrate;
Active-Site 162
[UniProt10]
UniProt: Proton acceptor; Non-Experimental Qualifier: probable;
Metal-Binding-Site 164
[UniProt10]
UniProt: Magnesium 3;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
7/10/1998 (pkarp) Merged genes G7581/b3034 and EG12633/yqiE
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Avison01: Avison MB, Horton RE, Walsh TR, Bennett PM (2001). "Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media." J Biol Chem 276(29);26955-61. PMID: 11350954

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

Badger05: Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ (2005). "Structural analysis of a set of proteins resulting from a bacterial genomics project." Proteins 60(4);787-96. PMID: 16021622

Bessman96: Bessman MJ, Frick DN, O'Handley SF (1996). "The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes." J Biol Chem 271(41);25059-62. PMID: 8810257

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

Dunn99: Dunn CA, O'Handley SF, Frick DN, Bessman MJ (1999). "Studies on the ADP-ribose pyrophosphatase subfamily of the nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance." J Biol Chem 274(45);32318-24. PMID: 10542272

Gabelli01: Gabelli SB, Bianchet MA, Bessman MJ, Amzel LM (2001). "The structure of ADP-ribose pyrophosphatase reveals the structural basis for the versatility of the Nudix family." Nat Struct Biol 8(5);467-72. PMID: 11323725

Gabelli02: Gabelli SB, Bianchet MA, Ohnishi Y, Ichikawa Y, Bessman MJ, Amzel LM (2002). "Mechanism of the Escherichia coli ADP-ribose pyrophosphatase, a Nudix hydrolase." Biochemistry 41(30);9279-85. PMID: 12135348

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."

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

Krisko14: Krisko A, Copi T, Gabaldon T, Lehner B, Supek F (2014). "Inferring gene function from evolutionary change in signatures of translation efficiency." Genome Biol 15(3);R44. PMID: 24580753

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Melo66: Melo A, Glaser L (1966). "Nucleotide diphosphate hexose pyrophosphatases." Biochem Biophys Res Commun 1966;22(5);524-31. PMID: 5330035

MorenoBruna01: Moreno-Bruna B, Baroja-Fernandez E, Munoz FJ, Bastarrica-Berasategui A, Zandueta-Criado A, Rodriguez-Lopez M, Lasa I, Akazawa T, Pozueta-Romero J (2001). "Adenosine diphosphate sugar pyrophosphatase prevents glycogen biosynthesis in Escherichia coli." Proc Natl Acad Sci U S A 98(14);8128-32. PMID: 11416161

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111


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 18.5 on Fri Nov 28, 2014, BIOCYC13B.