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The CoFactor database: Organic cofactors in enzyme catalysis.

01:46 EDT 20th April 2014 | BioPortfolio

Summary of "The CoFactor database: Organic cofactors in enzyme catalysis."


MOTIVATION:
Organic enzyme cofactors are involved in many enzyme reactions. Therefore, the analysis of cofactors is crucial to gain a better understanding of enzyme catalysis. To aid this, we have created the CoFactor database.
RESULTS:
CoFactor provides a web interface to access hand-curated data extracted from the literature on organic enzyme cofactors in biocatalysis, as well as automatically collected information. CoFactor includes information on the conformational and solvent accessibility variation of the enzyme-bound cofactors, as well as mechanistic and structural information about the hosting enzymes.
AVAILABILITY:
The database is publicly available and can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/CoFactor.
CONTACT:
julia.fischer@ebi.ac.uk.

Affiliation

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Journal Details

This article was published in the following journal.

Name: Bioinformatics (Oxford, England)
ISSN: 1367-4811
Pages:

Links

PubMed Articles [6364 Associated PubMed Articles listed on BioPortfolio]

Beyond the Protein Matrix: Probing Cofactor Variants in a Baeyer-Villiger Oxygenation Reaction.

A general question in biochemistry is the interplay between the chemical properties of cofactors and the surrounding protein matrix. Here, the functions of NADP(+) and FAD are explored by investigatio...

Recent trends and novel concepts in cofactor-dependent biotransformations.

Cofactor-dependent enzymes catalyze a broad range of synthetically useful transformations. However, the cofactor requirement also poses economic and practical challenges for the application of these b...

Substrate-Assisted O2 Activation in a Cofactor-Independent Dioxygenase.

In contrast to the majority of O2-activating enzymes, which depend on an organic cofactor or a metal ion for catalysis, a particular group of structurally unrelated oxygenases is functional without an...

Nitrogenase FeMo cofactor: an atomic structure in three simple steps.

The enzyme nitrogenase catalyzes the six-electron reduction of molecular dinitrogen to ammonium, concomitant with the reduction of protons to yield hydrogen gas. In the MoFe protein component of the n...

Insect Cell-Derived Cofactors Become Fully Functional after Proteinase K and Heat Treatment for High-Fidelity Amplification of Glycosylphosphatidylinositol-Anchored Recombinant Scrapie and BSE Prion Proteins.

The central event in prion infection is the conformational conversion of host-encoded cellular prion protein (PrP(C)) into the pathogenic isoform (PrP(Sc)). Diverse mammalian species possess the cofac...

Clinical Trials [647 Associated Clinical Trials listed on BioPortfolio]

Clinical Trial in Patients With Metastatic Colorectal Cancer

The objectives of this trial are to determine if CoFactor in combination with 5-FU are effective in the treatment of metastatic colorectal cancer and to determine the side effects observed...

Study of cPMP (Precusor Z) to Treat Molybdenum Cofactor Deficiency (MoCD) Type A

Molybdenum Cofactor Deficiency Type A (MoCD) is a very rare autosomal recessive disorder that is essentially fatal early in life. Naturally occurring cPMP is present in the body of all hea...

5-Fluorouracil Combined With CoFactor (5-10 Methylenetetrahydrofolate) in Treating Advanced Breast Cancer Patients

A multi-center, open-label, single-arm Phase II trial assessing the efficacy and safety of weekly bolus infusions of 5-fluorouracil combined with CoFactor (5-10 methylenetetrahydrofolate)...

Lactate Metabolism Study in HIV Infected Persons

Lactic acidosis is a potentially life-threatening disease associated with the treatment of chronic HIV infection. Although acidosis is rare, hyperlactatemia is common and may have long ter...

Pilot Study of Organic Nitrates on Endothelial Function in CAD Patients

Organic nitrates increase levels of circulating endothelial progenitor cells (Thum et al., Arterioscler Thromb Vasc Biol. 2007 Apr;27(4):748-54). Here, we want to test the effects of two d...

Medical and Biotech [MESH] Definitions

The protein components of enzyme complexes (HOLOENZYMES). An apoenzyme is the holoenzyme minus any cofactors (ENZYME COFACTORS) or prosthetic groups required for the enzymatic function.

An aldehyde oxidoreductase expressed predominantly in the LIVER; LUNGS; and KIDNEY. It catalyzes the oxidation of a variety of organic aldehydes and N-heterocyclic compounds to CARBOXYLIC ACIDS, and also oxidizes quinoline and pyridine derivatives. The enzyme utilizes molybdenum cofactor and FAD as cofactors.

Conversion of an inactive form of an enzyme to one possessing metabolic activity. It includes 1, activation by ions (activators); 2, activation by cofactors (coenzymes); and 3, conversion of an enzyme precursor (proenzyme or zymogen) to an active enzyme.

An iron-sulfur and MOLYBDENUM containing FLAVOPROTEIN that catalyzes the oxidation of nitrite to nitrate. This enzyme can use either NAD or NADP as cofactors. It is a key enzyme that is involved in the first step of nitrate assimilation in PLANTS; FUNGI; and BACTERIA. This enzyme was formerly classified as EC 1.6.6.2.

An enzyme found primarily in BACTERIA and FUNGI that catalyzes the oxidation of ammonium hydroxide to nitrite. It is an iron-sulfur HEME; FLAVOPROTEIN containing siroheme and can utilize both NAD and NADP as cofactors. This enzyme was formerly classified as EC 1.6.6.4.

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