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Background  DNA gyrase, an enzyme once thought to be unique to bacteria, is also found in some eukaryotic plastids including the apicoplast of Apicomplexa such as  Plasmodium falciparum  and  Toxoplasma gondii  which are important disease-causing organisms. DNA gyrase is an excellent target for antibacterial drugs, yet such antibacterials seem ineffective against Apicomplexa. Characterisation of the apicoplast gyrases would be a useful step towards understanding why this should be so. While purification of active apicoplast gyrase has proved impossible to date,  in silico  analyses have allowed us to discover differences in the apicoplast proteins. The resulting predicted structural and functional differences will be a first step towards development of apicoplast-gyrase specific inhibitors.    Results  We have carried out sequence analysis and structural predictions of the enzymes from the two species and find that  P. falciparum  gyrase lacks a GyrA box, but  T. gondii  may retain one. All proteins contained signal/transport peptides for localization to the apicoplast but  T. gondii  Gyrase B protein lacks the expected hydrophobic region. The most significant difference is in the GyrA C-terminal domain: While the cores of the proteins, including DNA binding and cleavage regions are essentially unchanged, both apicoplast gyrase A proteins have C-terminal domains that are significantly larger than bacterial counterparts and are predicted to have different structures.    Conclusion  The apicoplast gyrases differ significantly from bacterial gyrases while retaining similar core domains.  T. gondii  Gyrase B may have an unusual or inefficient mechanism of localisation to the apicoplast.  P.falciparum  gyrase, lacks a GyrA box and is therefore likely to be inefficient in DNA supercoiling. The C-terminal domains of both apicoplast Gyrase A proteins diverge significantly from the bacterial proteins. We predict that an additional structural element is present in the C-terminal domain of both apicoplast Gyrase A proteins, including the possibility of a β-pinwheel with a non-canonical number of blades. These differences undoubtedly will affect the DNA supercoiling mechanism and have perhaps evolved to compensate for the lack of Topoisomerase IV in the apicoplast. These data will be useful first step towards further characterisation and development of inhibitors for apicoplast gyrases.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-014-0416-9) contains supplementary material, which is available to authorized users.

Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum