Escherichia coli K-12 substr. MG1655 Enzyme: NADH pyrophosphatase

Gene: nudC Accession Numbers: EG11702 (EcoCyc), b3996, ECK3988

Synonyms: yjaD

Regulation Summary Diagram: ?

Regulation summary diagram for nudC

Subunit composition of NADH pyrophosphatase = [NudC]2
         NADH pyrophosphatase = NudC

NudC is active in decapping RNA molecules that have been capped at the 5' end with an NAD modification [Cahova15].

NudC belongs to the family of "Nudix" hydrolases [Bessman96]. Unlike other members of this family, which have nucleoside triphosphate pyrophosphohydrolase activity, it was shown to have NADH pyrophosphatase activity in vitro. The enzyme has a preference for NADH, the reduced form of the cofactor, as a substrate; its Km for NADH is 50-fold lower than its Km for NAD+ [Frick95a].

Based on sequence similarity, NudC was predicted to be a NAD+ diphosphatase [Reed03].

Reviews: [McLennan06, Luciano15]

Citations: [McLennan13]

Locations: cytosol

Map Position: [4,194,926 -> 4,195,699] (90.41 centisomes, 325°)
Length: 774 bp / 257 aa

Molecular Weight of Polypeptide: 29.689 kD (from nucleotide sequence), 29 kD (experimental) [Frick95a ]

Molecular Weight of Multimer: 60.0 kD (experimental) [Frick95a]

Unification Links: ASAP:ABE-0013063 , DIP:DIP-10373N , EchoBASE:EB1653 , EcoGene:EG11702 , EcoliWiki:b3996 , ModBase:P32664 , OU-Microarray:b3996 , PortEco:nudC , PR:PRO_000023421 , Protein Model Portal:P32664 , RefSeq:YP_026280 , RegulonDB:EG11702 , SMR:P32664 , String:511145.b3996 , UniProt:P32664

Relationship Links: InterPro:IN-FAMILY:IPR000086 , InterPro:IN-FAMILY:IPR015375 , InterPro:IN-FAMILY:IPR015376 , InterPro:IN-FAMILY:IPR015797 , InterPro:IN-FAMILY:IPR020084 , InterPro:IN-FAMILY:IPR022925 , PDB:Structure:1VK6 , PDB:Structure:2GB5 , Pfam:IN-FAMILY:PF00293 , Pfam:IN-FAMILY:PF09296 , Pfam:IN-FAMILY:PF09297 , Prosite:IN-FAMILY:PS00893 , Prosite:IN-FAMILY:PS51462

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006402 - mRNA catabolic process Inferred from experiment [Cahova15]
GO:0008152 - metabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01, GOA01a, Frick95a]
GO:0034661 - ncRNA catabolic process Inferred from experiment [Cahova15]
Molecular Function: GO:0030145 - manganese ion binding Inferred from experiment Inferred by computational analysis [GOA06, Frick95a]
GO:0035529 - NADH pyrophosphatase activity Inferred from experiment [Frick95a]
GO:0042803 - protein homodimerization activity Inferred from experiment [Frick95a]
GO:0000210 - NAD+ diphosphatase activity Inferred by computational analysis [GOA06, GOA01, GOA01a]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides

Essentiality data for nudC 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]

Created 18-May-2012 by Keseler I , SRI International
Last-Curated ? 07-May-2015 by Keseler I , SRI International

Enzymatic reaction of: NADH pyrophosphatase

EC Number:

NADH + H2O <=> NMNH + AMP + 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. [Frick95a]

Alternative Substrates for NADH: NAD+ [Frick95a ]

Cofactors or Prosthetic Groups: Mn2+ [Frick95a]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)

pH(opt): 8.5 [BRENDA14, Frick95a]

Sequence Features

Protein sequence of NADH pyrophosphatase with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 33
[Blattner93, UniProt10a]
UniProt: (in Ref. 2; AAC43094);
Metal-Binding-Site 98
UniProt: Zinc.
Metal-Binding-Site 101
UniProt: Zinc.
Metal-Binding-Site 116
UniProt: Zinc.
Metal-Binding-Site 119
UniProt: Zinc.
Conserved-Region 125 -> 248
UniProt: Nudix hydrolase;
Protein-Segment 159 -> 180
UniProt: Nudix box; Sequence Annotation Type: short sequence motif.
Metal-Binding-Site 174
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 178
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;

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 b3996 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11702; 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

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

Blattner93: Blattner FR, Burland V, Plunkett G, Sofia HJ, Daniels DL (1993). "Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes." Nucleic Acids Res 1993;21(23);5408-17. PMID: 8265357

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Cahova15: Cahova H, Winz ML, Hofer K, Nubel G, Jaschke A (2015). "NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs." Nature 519(7543);374-7. PMID: 25533955

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

Frick95a: Frick DN, Bessman MJ (1995). "Cloning, purification, and properties of a novel NADH pyrophosphatase. Evidence for a nucleotide pyrophosphatase catalytic domain in MutT-like enzymes." J Biol Chem 270(4);1529-34. PMID: 7829480

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Luciano15: Luciano DJ, Belasco JG (2015). "NAD in RNA: unconventional headgear." Trends Biochem Sci 40(5);245-7. PMID: 25801053

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

McLennan13: McLennan AG (2013). "Substrate ambiguity among the nudix hydrolases: biologically significant, evolutionary remnant, or both?." Cell Mol Life Sci 70(3);373-85. PMID: 23184251

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

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.

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."

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 Tue Oct 13, 2015, biocyc13.