UniProt release 2012_02

Headline

Thiamine thiazole synthase: enzyme, catalyst or co-substrate?

Thiamine is a cofactor essential for many biochemical reactions in all living beings. Humans depend on their diet to supply it as vitamin B1, while bacteria, plants and yeast can make their own. They do so by coupling two precursor molecules: a sulfur-containing ring structure known as a thiazole and a nitrogenous pyrimidine.

In eukaryotes, it has been known for some time that thiamine thiazole synthase catalyzes thiazole biosynthesis, but the source of the thiazole sulfur at the heart of the reaction remained elusive. A recent publication unveiled a very unusual mechanism, whereby a sulfide ion is transferred from a conserved cysteine of thiamine thiazole synthase itself to become part of the thiazole precursor in Saccharomyces cerevisiae. This transfer is strictly dependent on the presence of Fe(2+). The donor cysteine, Cys-205, is irreversibly converted to dehydroalanine, leading to the inactivation of the enzyme. Surprisingly the inactivated protein is not degraded, but accumulates in the cell where it can form up to about 1.5% of total cellular protein. Could it have another physiological function? This has yet to be explored, but it has been suggested to play a role in mitochondrial DNA damage tolerance.

Although very rare, the use of a protein as a metabolic reagent has already been observed. The best characterized example is methylated-DNA--protein-cysteine methyltransferase, which repairs O-6 alkylated guanine lesions in DNA by stoichiometrically transferring the alkyl group to a cysteine residue in the enzyme. Here again we face a suicidal reaction, the enzyme being irreversibly inactivated. Interestingly, the inactive enzyme serves as a signal to induce other DNA repair enzymes.

Can such proteins be considered as “enzymes”? An enzyme is defined as a protein that catalyzes chemical reactions of other substances without itself being destroyed or altered upon completion of the reactions. Thiamine thiazole synthase functions as a “one-shot” reagent, so therefore does not comply with the definition. At most it can be considered as a catalyst, i.e. a reagent which promotes a reaction and may act repeatedly or only once.

Such an unusual mechanism has led to some inconsistencies. The Enzyme Commission attributed the EC number 2.1.1.63 to methylated-DNA--protein-cysteine methyltransferases, mentioning the ambiguity of this attribution: “This enzyme catalyzes only one turnover and therefore is not strictly catalytic.” Actually the protein is a catalyst, but it is not strictly an enzyme. The later decision not to provide an EC number to thiamine thiazole synthases is more consistent in view of the definition of an enzyme. This inconsistency is also visible in UniProtKB entries which show EC numbers in the ‘Names and origin’ section of methylated-DNA--protein-cysteine methyltransferases, but not in that of thiamine thiazole synthases.

As of this release, thiamine thiazole synthases, have been updated in UniProtKB/Swiss-Prot and a new post-translational modification, 2,3-didehydroalanine has been introduced.

UniProtKB news

Update to the human proteome

The human reference proteome has been updated with data from Ensembl release 65. Ensembl 65 has numerous updates to the human genome including an update of Havana manual annotation representing data present in Vega release 45. As a result, the human reference proteome has increased in size by over 7,000 entries. These new entries correspond to fragment entries that have transcription evidence captured by Havana and as such they are considered valid members of the proteome. Two examples of these fragment entries are H0Y5B1 and H0Y653.

Change of the cross-reference GeneDB_Spombe to PomBase

The Schizosaccharomyces pombe GeneDB was replaced by PomBase, the new model organism database for the fission yeast Schizosaccharomyces pombe. We have therefore changed the corresponding resource abbreviation from GeneDB_SPombe to PomBase and the resource identifiers are now prefixed with PomBase:.

Change of the category of the cross-reference KO

The KO database has been moved from the category “Family and domain databases” to the category “Phylogenomic databases”.

Removal of the cross-reference NMPDR

Cross-references to NMPDR have been removed.

Changes to the controlled vocabulary for PTMs

New terms for the feature key ‘Modified residue’ (‘MOD_RES’ in the flat file):

• 2,3-didehydroalanine (Cys)
• N6-malonyllysine