Bioinformatic analysis of β/α-barrel fold basic amino acid decarboxylases
This example is discussed in detail in Suplatov (2013) J Biomol Struct Dyn

Pyridoxal 5΄-phosphate (PLP)-dependent basic amino acid decarboxylases from the β/α-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates essential for polyamine and lysine biosynthesis (Deng, 2010). This family of PLP-dependent enzymes functions on a broad range of basic amino acid substrates required for polyamine biosynthesis and includes ornithine decarboxylases (ODC), arginine decarboxylases (ADC), diaminopimelate decarboxylases (DAPDC) and carboxynorspermidine decarboxylases (CANSDCs). Thus, the family of β/α-barrel-fold basic amino acid decarboxylases provides an excellent model to study molecular basis of substrate specificity within a conserved structural fold.

Zebra identified three subfamilies corresponding to ADCs, CANSDCs, DAPDCs and two subfamilies for ODCs (five subfamilies in total), and suggested 32 positions as subfamily-specific (Tables 1). Significant hits S325, N327, C328, I329, Y331, D332, and H333 are part of so-called 3`10-alpha-helix that is located to one side of the substrate-binding cavity of TbODC. Structural analysis of the 3`10-helix revealed that it has alternative orientations in enzymes with different substrate preference. The increased bulk of the amino acid side chain in specific position G393 correlates with the fact that 3`10-helix is shifted further back in the pocket in ADCs and DAPDCs compared to ODCs: ODC enzymes have small hydrophobic residues Ala and Gly in positions homologous to G393 of TbODC, while ADCs and DAPDCs have Leu and Met respectively. ODCs have the shortest ligand (L-ornithine) while ADCs and DAPDCs have to accommodate ligands of larger size (L-arginine and diaminopimelate, respectively). It seems that the distance between PLP cofactor and 310-helix is used to restrict catalysis to a ligand of correct size and residue in the specific position G393 can accommodate this mechanism in the family.

Since most residues within or close to 3`10-helix were identified as highly significant SSPs this structural element is suggested as a key specificity factor for discrimination of substrate preference probably by providing specific interaction profile and accommodating different flexibility of the helix. This suggestion is in a full agreement with previously published results (Deng, 2010; Lee, 2007; Shah, 2007) and reveals previously unknown positions for further study.

Output Zebra file: download

Table 1. Subfamily-specific positions in β/α-barrel fold basic amino acid decarboxylases family of enzymes. Click to enlarge.

Subfamily-specific positions in β/α-barrel fold basic amino acid decarboxylases enzyme family (ranks 1 to 19). Hits are ranked in decline of statistical significance. Positions are given based on numbering in ornithine decarboxylase from Trypanosoma brucei ([PDB:1F3T]). Positions from the catalytic site are marked with ‘*’. For every subfamily at least 90% of occurring residues are shown.