**3.3 KARI modeling**

The modeling of KARI enzyme from *N. gonorrhoeae* was carried out using the Swiss-model webserver, using as a template the KARI enzyme from *Staphylococcus aureus* (PDBID 5w3k). As shown in **Figure 5**, the KARI model shows high similarity in the active pocket (AFAHGFNIH) and N-terminal and C-terminal domains. A Neisseria gonorrhoeae *Ketol-Acid Reductoisomerase Is a Potential Therapeutic Target DOI: http://dx.doi.org/10.5772/intechopen.107993*

## **Figure 5.**

*Comparison of the crystal structure of the Ng KARI (model) with Sa KARI-Mg2+-NADPH-CPD complex. (a) Mg2+ ions (blue), and NADPH (red) are shown, respectively, as spheres and sticks. In (b) the Mg2+ ions (yellow) are drawn as spheres. The residues colored in red in Sa KARI (i.e. residues 131–145) and magenta in Ng KARI (i.e. residues 130–144) have different orientations in the two enzymes, probably due to the binding of NADPH.*

comparison of the N-terminal section of *Ng* KARI with the *Sa* KARI shows that they are some prominent structural differences, particularly in the region from *Ng* KARI as illustrated in **Figure 5**.

The overall fold of the *Ng* KARI resembles that of the *Sa* KARI-NADP(H) complex. No significant domain movements are observed between these two enzymes apart from a change in orientation of the polypeptide associated with the NADP(H) binding site. KARIs from class I differ in their quaternary structures by being dimeric like *Ng* KARI, *Sa* KARI, and KARI from *Mycobacterium tuberculosis* (*Mt* KARI), while others like KARI from *Campylobacter jejuni* (*Cj* KARI) are dodecameric. In their respective active sites, there are two differences between *Ng* KARI and *Sa* KARI, i.e., G100/A106 and L103/ F109. These differences are conserved between *Ng* KARI and *Mt* KARI, G100/G104, L103/L107, with G130/G129. The catalytic residue E230 and Mg2+ ligands are highly conserved between all tested pathogens.
