Arylformamidase Introduction

The structure 2PBL, as denoted by its Protein Data Bank (PDB) accession number, was determined using x-ray crystallography at the Joint Center for Structural Genomics (JCSG) (see figure 2). 2PBL heralds from Silicibacter sp. TM1040, a member of the Roseobacter clade of alpha-proteobacteria. One of the goals of the JCSG is to achieve structural coverage of a broad range of protein families by analysing homologous sequences from a variety of model organisms which includes Silicibacter sp. For structural determination, the protein was expressed in Escherichia coli using a plasmid as the vector. A resolution of 1.79A was achieved with an R-value of 0.224 and an R-free value of 0.270, all of which are indiciative of a high-quality structure.

Figure 2: An overview of 2PBL exhibiting all chains: A - upper right, B - upper left, C - lower right & D - lower left. The red molecule in the chain structure represents an unknown ligand. The molecules in the middle of chains A & B and chains C & D is a phosphate ion (PO4). The green molecule between chains B & D is a magnesium ion (Mg). Image generated using PDB ProteinWorkshop 1.5.

Upon crystallisation, 2PBL formed a tetramer structure. However, structures which form upon crystalisation do not always denote the functional form of a protein which can exist as a dimer or oligomer as well. In fact, such forms may have been evolutionarily selected for to confer features such as thermostability (Byun 2007).

Silicibacter sp. TM1040 was first isolated as part of an investigation into the role of bacteria in the physiology and toxigenesis of the dinoflagellate Pfiestera piscicida. Silicibacter sp. TM1040 has been found necessary for the survival of this organism. Most interestingly, the bacteria is able to demethylate the dinoflagellate secondary metabolite dimethylsulfoniopropionate (DMSP) to methylmercaptopropionic acid (MMPA). DMSP is the major source of organic sulphur in the world’s oceans, forming a major part of the global sulphur cycle.

A putative name 'arylformamidase' was assigned to the structure 2PBL based upon its closest mammalian homologue of the same name. Why a name based upon its mammalian homologue was assigned for a protein from such a distantly-related ancestral species remains unclear. Arylformamidase in mammals is a protein involved in the tryptophan degradation pathway. Whether this name accurately reflects the protein's function in bacteria needs to be assessed.

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