**9. Diaminopimelate decarboxylase**

#### **9.1 Function of DAPDC**

*Diaminopimelate decarboxylase* (DAPDC, EC 4. 1. 1. 20) is a PLP-dependant enzyme that is responsible for catalysing the final reaction of the lysine biosynthesis pathway (Fig. 1). In this non-reversible reaction, DAPDC converts the substrate *meso-*DAP to lysine and carbon dioxide (Fig. 21). Unlike other PLP-dependant decarboxylases that decarboxylate an *L*-stereocentre, DAPDC specifically cleaves the *D*-stereocentre carboxyl group. Thus, the enzyme possesses a means to differentiate between two stereocentres (Gokulan et al., 2003; Ray et al., 2002). DAPDC is classified as a type III class PLP enzyme, from the alanine racemase family.

Fig. 21. DAPDC catalysed reaction.

Compared to other enzymes within the lysine biosynthesis pathway, DAPDC has not been studied extensively. Consequently, the catalytic mechanism is poorly defined. However, current understanding of the structure and function of this enzyme is based on work performed on DAPDC from *Helicobacter pylori* (Hu et al., 2008)*, M. tubercolosis* (Weyand et al., 2009)*,* and *Methanococcus jannaschii* (Ray et al., 2002)*.*

#### **9.2 Structure of DAPDC**

The crystal structures of DAPDC from seven species have been determined. There appears to be no consensus in quaternary structure of the enzyme as monomeric, dimeric, and tetrameric forms of DAPDC have been described. This is unusual, and possibly not a true reflection of what occurs in nature. Studies have shown that the active site of DAPDC is located at the dimer interface (Hu et al., 2008; Ray et al., 2002; Weyand et al., 2009). This implies that the dimer is the minimal catalytic unit. Therefore, monomeric forms of DAPDC are likely to be non-functional; however, this does not rule out the existence of active tetrameric forms of DAPDC.

In species such as *M. jannaschii* (Ray et al., 2002) and *M. tubercolosis,* (Gokulan et al., 2003; Weyand et al., 2009) DAPDC is composed of a homodimer, whereby subunits associate to form a head-to-tail quaternary architecture (Fig. 22).

Fig. 22. Structure of *M. tuberculosis* DAPDC. (A) *M. tuberculosis* DAPDC monomer - The Nterminal (purple) and C-terminal (grey) domains are indicated. (B) *M. tuberculosis* DAPDC dimer – The active site is situated at the homodimer interface. PLP (yellow) and lysine (yellow) are located within the active site cavity (PDB: 1HKV).

are likely to be non-functional; however, this does not rule out the existence of active

In species such as *M. jannaschii* (Ray et al., 2002) and *M. tubercolosis,* (Gokulan et al., 2003; Weyand et al., 2009) DAPDC is composed of a homodimer, whereby subunits associate to

(A)

(B) Fig. 22. Structure of *M. tuberculosis* DAPDC. (A) *M. tuberculosis* DAPDC monomer - The Nterminal (purple) and C-terminal (grey) domains are indicated. (B) *M. tuberculosis* DAPDC dimer – The active site is situated at the homodimer interface. PLP (yellow) and lysine

(yellow) are located within the active site cavity (PDB: 1HKV).

tetrameric forms of DAPDC.

form a head-to-tail quaternary architecture (Fig. 22).

The DAPDC monomer is composed of two domains, consisting of an N-terminal 8-fold α/βbarrel domain and a C-terminal β-sheet domain (Gokulan et al., 2003; Ray et al., 2002) (Fig. 22A). In *M. tuberculosis* DAPDC, the N-terminal α/β-barrel domain (residues 48-308) is comprised of β-strands β4–β13 and helices α2-α10 (Fig. 22A). The C-terminal domain (residues 2-47 and 309-446) is comprised of β-strands β1-β3, β14-β21 and helices α1, α11-α13 (Gokulan et al., 2003) (Fig. 22A). The active site is located at the interface between the α/β-barrel domain of one subunit and β-sheet domain of both subunits (Gokulan et al., 2003) (Fig. 22B).

The X-ray structure of *H. pylori* DAPDC has allowed identification of key residues involved in substrate and cofactor recognition. The enzyme was crystallised in the presence of PLP and lysine. The *H. pylori* structure is very similar to that of *M. tuberculosis* DAPDC, forming a homodimer in a head-to-tail conformation. In this enzyme, PLP forms Schiff base linkages with Lys46 and lysine to produce a lysine-PLP external aldimine. This aldimine is believed to mimic the catalytic intermediate formed between *meso*-DAP and PLP (Hu et al., 2008).
