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



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

Synonyms: yjaD

Regulation Summary Diagram: ?

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

Summary:
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. 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+ [Frick95].

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

Review: [McLennan06]

Locations: cytosol

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

Molecular Weight of Polypeptide: 29.689 kD (from nucleotide sequence), 29 kD (experimental) [Frick95 ]

Molecular Weight of Multimer: 60.0 kD (experimental) [Frick95]

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: ?

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Frick95, UniProtGOA11, GOA06, GOA01a, GOA01]
Molecular Function: GO:0030145 - manganese ion binding Inferred from experiment Inferred by computational analysis [GOA06, Frick95]
GO:0035529 - NADH pyrophosphatase activity Inferred from experiment [Frick95]
GO:0000210 - NAD+ diphosphatase activity Inferred by computational analysis [GOA06, GOA01a, GOA01]
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 [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA01]
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]

Credits:
Created 18-May-2012 by Keseler I , SRI International
Last-Curated ? 18-May-2012 by Keseler I , SRI International


Enzymatic reaction of: NADH pyrophosphatase

EC Number: 3.6.1.9

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. [Frick95]

Alternative Substrates for NADH: NAD+ [Frick95 ]

Cofactors or Prosthetic Groups: Mn2+ [Frick95]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
NADH
110.0
0.001
[Frick95, BRENDA14]
NAD+
5100.0
[Frick95]

pH(opt): 8.5 [BRENDA14, Frick95]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 33
[Blattner93, UniProt10a]
Alternate sequence: A → R; UniProt: (in Ref. 2; AAC43094);
Metal-Binding-Site 98
[UniProt10a]
UniProt: Zinc;
Metal-Binding-Site 101
[UniProt10a]
UniProt: Zinc;
Metal-Binding-Site 116
[UniProt10a]
UniProt: Zinc;
Metal-Binding-Site 119
[UniProt10a]
UniProt: Zinc;
Conserved-Region 125 -> 248
[UniProt09]
UniProt: Nudix hydrolase;
Protein-Segment 159 -> 180
[UniProt10a]
UniProt: Nudix box; Sequence Annotation Type: short sequence motif;
Metal-Binding-Site 174
[UniProt10a]
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 178
[UniProt10a]
UniProt: Divalent metal cation; Non-Experimental Qualifier: by similarity;


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 ].
10/20/97 Gene b3996 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11702; confirmed by SwissProt match.


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

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." http://www.brenda-enzymes.org.

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

Frick95: 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, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

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.

UniProtGOA11: 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 Sun Nov 23, 2014, biocyc14.