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



Gene: nudE Accession Numbers: G7740 (EcoCyc), b3397, ECK3384

Synonyms: yrfE

Regulation Summary Diagram: ?

Subunit composition of ADP-sugar pyrophosphorylase = [NudE]2
         ADP-sugar pyrophosphorylase = NudE

Summary:
NudE belongs to the family of Nudix hydrolases [Bessman96]. The enzyme is specific for nucleoside pyrophosphates with an ADP moiety; preferred substrates of NudE include adenosine(5')triphospho(5')adenosine (Ap3A), ADP-ribose, and NADH [OHandley98].

Gel filtration experiments suggest that the enzyme is a dimer in solution [OHandley98]. A crystal structure has been solved at 2.32 Å resolution [Badger05].

An mrcA nudE yrfF triple mutant exhibits phenotypes including mucoidy, heat sensitivity, growth defects, and resistance to phage or antibiotic drugs, whereas a single mrcA mutant does not [Meberg01].

Expression of nudE may be regulated by ArcA [Federowicz14].

Review: [McLennan06]

Locations: cytosol

Map Position: [3,523,611 <- 3,524,171] (75.95 centisomes)
Length: 561 bp / 186 aa

Molecular Weight of Polypeptide: 21.153 kD (from nucleotide sequence), 21.5 kD (experimental) [OHandley98 ]

Molecular Weight of Multimer: 43.0 kD (experimental) [OHandley98]

Unification Links: ASAP:ABE-0011086 , DIP:DIP-10374N , EchoBASE:EB2762 , EcoGene:EG12926 , EcoliWiki:b3397 , ModBase:P45799 , OU-Microarray:b3397 , PortEco:nudE , PR:PRO_000023423 , Pride:P45799 , Protein Model Portal:P45799 , RefSeq:NP_417856 , RegulonDB:G7740 , SMR:P45799 , String:511145.b3397 , Swiss-Model:P45799 , UniProt:P45799

Relationship Links: InterPro:IN-FAMILY:IPR000086 , InterPro:IN-FAMILY:IPR015797 , InterPro:IN-FAMILY:IPR020084 , PDB:Structure:1VHG , PDB:Structure:1VHZ , Pfam:IN-FAMILY:PF00293 , Prosite:IN-FAMILY:PS00893 , Prosite:IN-FAMILY:PS51462

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [OHandley98, UniProtGOA11a, GOA01a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [OHandley98]
GO:0019144 - ADP-sugar diphosphatase activity Inferred from experiment [OHandley98]
GO:0042803 - protein homodimerization activity Inferred from experiment [OHandley98]
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, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism

Essentiality data for nudE 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]

Credits:
Last-Curated ? 27-Aug-2014 by Keseler I , SRI International


Enzymatic reaction of: ADP-sugar pyrophosphorylase

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 direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for an ADP-sugar: NADH [OHandley98 ] , ADP-D-ribose [OHandley98 ] , 5',5'''-diadenosine triphosphate [OHandley98 ]

Cofactors or Prosthetic Groups: Mg2+ [OHandley98]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
5',5'''-diadenosine triphosphate
1.5e-4
11.1
[OHandley98]
ADP-D-ribose
2.2e-4
9.9
[OHandley98]
NADH
1.2e-4
7.8
[OHandley98]

pH(opt): 9.0 [OHandley98]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 40
[UniProt10a]
UniProt: Substrate; via amide nitrogen and carbonyl oxygen;
Conserved-Region 45 -> 172
[UniProt09]
UniProt: Nudix hydrolase;
Protein-Segment 80 -> 101
[UniProt10a]
UniProt: Nudix box; Sequence Annotation Type: short sequence motif;
Metal-Binding-Site 95
[UniProt10a]
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 99
[UniProt10a]
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 118
[UniProt10a]
UniProt: Substrate; via carbonyl oxygen;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Federowicz14: Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho BK, Zengler K, Palsson B (2014). "Determining the control circuitry of redox metabolism at the genome-scale." PLoS Genet 10(4);e1004264. PMID: 24699140

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

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

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

McLennan06: McLennan AG (2006). "The Nudix hydrolase superfamily." Cell Mol Life Sci 63(2);123-43. PMID: 16378245

Meberg01: Meberg BM, Sailer FC, Nelson DE, Young KD (2001). "Reconstruction of Escherichia coli mrcA (PBP 1a) mutants lacking multiple combinations of penicillin binding proteins." J Bacteriol 183(20);6148-9. PMID: 11567017

OHandley98: O'Handley SF, Frick DN, Dunn CA, Bessman MJ (1998). "Orf186 represents a new member of the Nudix hydrolases, active on adenosine(5')triphospho(5')adenosine, ADP-ribose, and NADH." J Biol Chem 273(6);3192-7. PMID: 9452430

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

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

UniProt10a: 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."


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 Sat Dec 20, 2014, biocyc12.