Note_Cofactors – Cofactors

WID Note_Cofactors
Name Cofactors
Comments Reaction coenzymes and prosthetic groups were reconstructed from several sources including the databases BioCyc [PUB_0006], BRENDA [PUB_0570], GenoBase [PUB_0386], Kinetikon [PUB_0571], Metal-MaCiE [PUB_0387], and UniProt [PUB_0096] and the primary literature [PUB_0131]. These sources frequently report protein prosthetic groups as a list of chemical species (eg. metal ions) which can each fill the same prosthetic group role. We simplified these ambiguous lists of possible prosthetic groups to a single chemical species by choosing the most common chemical species according to cell composition (Na+, K+ > Mg2+, Cl- > Fe2+, Fe3+ > Ca2+ > Mn2+ > Cu2+ > Mo6+, Zn2, Co2, Ni2 [PUB_0393, PUB_0394, PUB_0395]), or the species with the highest protein affinity (Irving-Williams Series, Mn2+ < Fe2+, Fe3+ < Co2+ < Ni2+ < Cu2+ > Zn2+ [PUB_0404]).
  1. . Kinetikon. (None). WholeCell: PUB_0571, URL:

  2. Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics 25, 2088-9 (2009). WholeCell: PUB_0387, PubMed: 19369503, URL:

  3. Boschi-Muller S, Olry A, Antoine M, Branlant G. The enzymology and biochemistry of methionine sulfoxide reductases. Biochim Biophys Acta 1703, 231-8 (2005). WholeCell: PUB_0131, PubMed: 15680231

  4. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 37, D588-92 (2009). WholeCell: PUB_0570, PubMed: 18984617

  5. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37, D464-70 (2009). WholeCell: PUB_0006, PubMed: 18974181

  6. ... 5 more

  7. Neidhardt FC, Ingraham JL, Schaechter M. Physiology of the Bacterial Cell: A Molecular Approach. Sinauer Associates Inc (1990). WholeCell: PUB_0393, ISBN: 9780878936083

  8. Pirt SJ. . (1975). WholeCell: PUB_0395, None

  9. Sundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res 32, D293-5 (2004). WholeCell: PUB_0394, PubMed: 14681416, URL:

  10. Tottey S, Waldron KJ, Firbank SJ, Reale B, Bessant C, Sato K, Cheek TR, Gray J, Banfield MJ, Dennison C, Robinson NJ. Protein-folding location can regulate manganese-binding versus copper- or zinc-binding. Nature 455, 1138-42 (2008). WholeCell: PUB_0404, PubMed: 18948958

  11. UniProt Consortium. The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res 37, D169-74 (2009). WholeCell: PUB_0096, PubMed: 18836194, URL:

Created 2012-10-01 15:07:34
Last updated 2012-10-01 15:13:57