Escherichia coli K-12 substr. MG1655 Enzyme: NAD kinase

Gene: nadK Accession Numbers: EG12192 (EcoCyc), b2615, ECK2611

Synonyms: yfjE, yfjB

Regulation Summary Diagram: ?

Regulation summary diagram for nadK

Subunit composition of NAD kinase = [NadK]6
         NAD kinase monomer = NadK

NAD kinase appears to be an allosteric enzyme, with activity tightly coupled to the NADPH/NADP+ and NADH/NAD+ ratios present in the cell. That suggests that NAD kinase may play an important role in the regulation of NADP turnover and size of the NADP pool [Zerez87, Kawai01].

nadK is likely essential for growth [Gerdes02, Baba06].

Site-directed mutagenesis studies of the E. coli enzyme showed that a R175G mutation relaxed the strict NAD substrate specificity of the enzyme, resulting in a low level of ATP-dependent NADH kinase activity [Mori05].

Structure-function relationships in NAD kinases from archaea, bacteria (including E. coli) and eukaryotes have been reviewed [Magni06, Kawai08, Shi09].

Locations: cytosol

Map Position: [2,748,853 -> 2,749,731] (59.25 centisomes, 213°)
Length: 879 bp / 292 aa

Molecular Weight of Polypeptide: 32.566 kD (from nucleotide sequence), 30 kD (experimental) [Kawai01 ]

Molecular Weight of Multimer: 180.0 kD (experimental) [Kawai01]

Unification Links: ASAP:ABE-0008603 , DIP:DIP-48103N , EchoBASE:EB2109 , EcoGene:EG12192 , EcoliWiki:b2615 , OU-Microarray:b2615 , PortEco:nadK , Pride:P0A7B3 , Protein Model Portal:P0A7B3 , RefSeq:NP_417105 , RegulonDB:EG12192 , SMR:P0A7B3 , String:511145.b2615 , Swiss-Model:P0A7B3 , UniProt:P0A7B3

Relationship Links: InterPro:IN-FAMILY:IPR002504 , InterPro:IN-FAMILY:IPR016064 , InterPro:IN-FAMILY:IPR017437 , InterPro:IN-FAMILY:IPR017438 , Panther:IN-FAMILY:PTHR20275 , Pfam:IN-FAMILY:PF01513

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006741 - NADP biosynthetic process Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Kawai01]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
GO:0019674 - NAD metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003951 - NAD+ kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Kawai01]
GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Mori05]
GO:0042802 - identical protein binding Inferred from experiment [Kawai01]
GO:0051287 - NAD binding Inferred from experiment [Mori05]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Watt07]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers nicotinamide adenine dinucleotide

Essentiality data for nadK knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Curated 01-Aug-2008 by Keseler I , SRI International
Last-Curated ? 22-Mar-2010 by Fulcher C , SRI International

Enzymatic reaction of: NAD kinase

Synonyms: ATP:NAD+ 2'-phosphotransferase, ATP-NAD kinase

EC Number:

ATP + NAD+ <=> ADP + NADP+ + H+

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 ATP: dTTP [Kawai01 ] , GTP [Kawai01 ] , dATP [Kawai01 ] , UTP [Kawai01 ] , CTP [Kawai01 ]

In Pathways: NAD phosphorylation and dephosphorylation I

The enzyme catalyzes the ATP-dependent phosphorylation of NAD+ and has strict substrate specificity for NAD+ [Mori05].

Cofactors or Prosthetic Groups: Mg2+ [Kawai01, Zerez87]

Inhibitors (Allosteric): NADH [Kawai01, Zerez87] , NADPH [Kawai01, Zerez87]

Primary Physiological Regulators of Enzyme Activity: NADH , NADPH

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Mori05, BRENDA14]
[Kawai01, BRENDA14]
[Mori05, BRENDA14]
[Kawai01, BRENDA14]

T(opt): 60 °C [BRENDA14, Kawai01]

pH(opt): 7.5 [Kawai01]

Sequence Features

Protein sequence of NAD kinase monomer with features indicated

Feature Class Location Attached Group Citations Comment
Active-Site 73  
UniProt: Proton acceptor.
Nucleotide-Phosphate-Binding-Region 73 -> 74 NAD+
UniProt: NAD.
Nucleotide-Phosphate-Binding-Region 147 -> 148 NAD+
UniProt: NAD.
Amino-Acid-Sites-That-Bind 158  
UniProt: NAD.
Amino-Acid-Sites-That-Bind 175  
UniProt: NAD.
Mutagenesis-Variant 175  
[Mori05, UniProt14a]
[Mori05, UniProt14a]
[Mori05, UniProt14a]
R → E, I or K: Does not exhibit NADH kinase activity in addition to NAD kinase activity.
R → H, Q or T: Exhibits NADH kinase activity in addition to NAD kinase activity.
R → G: Exhibits NADH kinase activity in addition to NAD kinase activity. Reduces the Vmax of the NAD kinase activity.
Amino-Acid-Sites-That-Bind 177  
UniProt: NAD.
Amino-Acid-Sites-That-Bind 185  
UniProt: NAD; via carbonyl oxygen.
Nucleotide-Phosphate-Binding-Region 188 -> 193 NAD+
UniProt: NAD.
Amino-Acid-Sites-That-Bind 247  
UniProt: NAD.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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 ].
10/20/97 Gene b2615 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12192; 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

Gerdes02: Gerdes SY, Scholle MD, D'Souza M, Bernal A, Baev MV, Farrell M, Kurnasov OV, Daugherty MD, Mseeh F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY, Chowdhury SA, Fonstein MY, Osterman AL (2002). "From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways." J Bacteriol 184(16);4555-72. PMID: 12142426

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."

Imsande62: Imsande J, Pardee AB (1962). "Regulation of pyridine nucleotide biosynthesis in Escherichia coli." J Biol Chem 237(4):1305-8.

Kawai01: Kawai S, Mori S, Mukai T, Hashimoto W, Murata K (2001). "Molecular characterization of Escherichia coli NAD kinase." Eur J Biochem 268(15);4359-65. PMID: 11488932

Kawai08: Kawai S, Murata K (2008). "Structure and function of NAD kinase and NADP phosphatase: key enzymes that regulate the intracellular balance of NAD(H) and NADP(H)." Biosci Biotechnol Biochem 72(4);919-30. PMID: 18391451

Magni06: Magni G, Orsomando G, Raffaelli N (2006). "Structural and functional properties of NAD kinase, a key enzyme in NADP biosynthesis." Mini Rev Med Chem 6(7);739-46. PMID: 16842123

Mori05: Mori S, Kawai S, Shi F, Mikami B, Murata K (2005). "Molecular conversion of NAD kinase to NADH kinase through single amino acid residue substitution." J Biol Chem 280(25);24104-12. PMID: 15855156

Reed03: Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)." Genome Biol 4(9);R54. PMID: 12952533

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

Shi09: Shi F, Li Y, Wang X (2009). "Molecular properties, functions, and potential applications of NAD kinases." Acta Biochim Biophys Sin (Shanghai) 41(5);352-61. PMID: 19430699

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Watt07: Watt RM, Wang J, Leong M, Kung HF, Cheah KS, Liu D, Danchin A, Huang JD (2007). "Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes." Nucleic Acids Res 35(6);e37. PMID: 17272300

Zerez87: Zerez CR, Moul DE, Gomez EG, Lopez VM, Andreoli AJ (1987). "Negative modulation of Escherichia coli NAD kinase by NADPH and NADH." J Bacteriol 1987;169(1);184-8. PMID: 3025169

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 Sun Oct 4, 2015, BIOCYC14A.