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The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
The subsystem approach is described, the first release of the growing library of populated subsystems is offered, and the SEED is the first annotation environment that supports this model of annotation.
The structural and biochemical foundations of thiamin biosynthesis.
Two thiamin degrading enzymes have been characterized and one of which is linked to a novel salvage pathway that can be salvaged through several routes, and the thiazole and pyrimidine moieties are synthesized in separate branches of the pathway.
Thiamin biosynthesis in prokaryotes
The X-ray structures of thiamin phosphate synthase and 5-hydroxyethyl-4-methylthiazole kinase have been completed and the genes coding for the thienin transport system (thiBPQ) have been identified.
NAD biosynthesis: identification of the tryptophan to quinolinate pathway in bacteria.
Saccharomyces cerevisiae THI4p is a suicidal thiamin thiazole synthase
The preparation of fully active recombinant wild-type THI4p is reported, the identification of an iron-dependent sulphide transfer reaction from a conserved cysteine residue of the protein to a reaction intermediate and the demonstration that THI 4p is a suicide enzyme undergoing only a single turnover are reported.
Reconstitution and biochemical characterization of a new pyridoxal-5'-phosphate biosynthetic pathway.
- K. Burns, Yun Xiang, C. Kinsland, F. McLafferty, T. Begley
- Chemistry, BiologyJournal of the American Chemical Society
- 1 March 2005
The substrates for Bacillus subtilis PLP synthase (YaaD and YaaE) are identified, and the first reconstitution of PLP biosynthesis using this pathway is described. Three partial reactions catalyzed…
High-resolution solution structures of oxidized and reduced Escherichia coli thioredoxin.
Structural insights into the mechanism of the PLP synthase holoenzyme from Thermotoga maritima.
- F. Zein, Yan Zhang, You-Na Kang, K. Burns, T. Begley, S. Ealick
- Biology, ChemistryBiochemistry
- 12 December 2006
An ammonia channel that connects the active site of YaaE with the ribulose 5-phosphate binding site was identified and is similar to one found in imidazole glycerol phosphate synthase; however, when the beta-barrels of the two complexes are superimposed, the glutaminase domains are rotated by about 180 degrees with respect to each other.
Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily.
Structural comparisons reveal that HMP-P synthase is homologous to a group of adenosylcobalamin radical enzymes, which supports an evolutionary relationship between these two superfamilies.
Structural studies on 3-hydroxyanthranilate-3,4-dioxygenase: the catalytic mechanism of a complex oxidation involved in NAD biosynthesis.
On the basis of the crystal structures of HAD, mutagenesis studies were carried out in order to elucidate the enzyme mechanism and a new mechanism for the enzyme inactivation by 4-chloro-3-hydroxyanthranilate is proposed.