The high resolution crystal structure of MPT synthase shows the enzyme has a heterotetrametric structure composed of two small subunits (MoaD in prokaryotes) and two large subunits (MoaE in prokaryotes) with the small subunits at opposite ends of a central large subunit dimer.^[1][4][5] The C-terminus of each small subunit is inserted into a large subunit to form the active site.^[4] In the enzyme's activated form the C-terminus is present as a thiocarboxylate, which acts as the sulfur donor to precursor Z in MoCo biosynthesis.^[4] As a result, the active site of the enzyme must be in close proximity to the C-terminus of the small subunit (i.e. MoaD in prokaryotes). The high resolution crystal structure of the enzyme also reveals the presence of a binding pocket for the terminal phosphate of molybdopterin and suggests a possible binding site for the pterin moiety present both in precursor Z and molybdopterin.^[8]

The structural similarity between ubiquitin and the small subunit of MPT synthase hints at the evolutionary relationship of the MoCo biosynthesis pathway and the ubiquitin dependent protein degradation pathway.^[4][9] Specifically, the small subunit MoaD in prokaryotes is a sequence homolog of Urm1, indicating that MPT synthase probably shares a common ancestor with ubiquitin.^[9]

The biosynthesis of MoCo is an old and evolutionary conserved pathway present in eukaryotes, eubacteria, and archea, which can be divided into three major steps.^[4] The first step involves the conversion of a guanosine nucleotide into precursor Z.^[4][10] In the following step, MPT synthase catalyzes the incorporation of the dithiolene moiety  to precursor Z, which converts it to molybdopterin.^[4] More specifically, this interconversion involves the opening of the cyclic phosphate ring of precursor Z, and the addition of two side chain sulfhydryl groups.^[10] E-coli MPT synthase is activated by the formation of a thiocarboxylate group at the second glycine of its C-terminal Gly-Gly motif, which serves as the sulfur donor for the formation of the diothiolene group in MPT.^[5][11] That is, the mechanism on MPT synthase depends on the interconversion between the activated form of MoaD with the thiocarboxylate group and the MoaE protein^[8] In the final step of MoCo biosynthesis, molybendum is incorporated to MPT by the two-domain protein gephyrin.^[5][6] MPT synthase sulfurylase recharges MPT synthase with a sulfur atom after each catalytic cycle.^[9]

MPT synthase is involved in the biosynthesis of MoCo, which is essential for the activity of enzymes like xanthine dehydrogenase, aldehyde oxidase, and sulfite oxidase in humans.^[5] MoCo containing enzymes typically catalyze the net transfer of an oxygen atom to and from  their substrates in a two electron redox reaction.^[4]

MoCo deficiency in humans results in the combined deficiency of the MoCo-containing enzymes: sulfite oxidase, xanthine oxidase, and aldehyde oxidase.^[4][5][7] Symptoms of MoCo deficiency are linked to the accumulation of toxic metabolites caused by the reduced activity of these molybdoenzymes, especially sulfite oxidase.^[4] Genetic defects in MoCo biosynthesis lead to MoCo deficiency.^[4] These genetic defects affect the formation of precursor Z (known as group A MoCo deficiency) or the conversion of precursor Z to MoCo by MPT synthase (known as group B MoCo deficiency).^[7][12] MOCS1 is defective for group A (the majority of patients), and encodes two enzymes involved in the formation of precursor Z.^[7][12] MOCS2 is defective for group B and encodes the small and large subunits of MPT synthase.^[7][12] Groups A and B of deficiency show an identical phenotype, characterized by neonatal seizures, attenuated brain growth, dislocated ocular lenses, feeding difficulties, among other neurological symptoms.^{[4][5][6][7][12]} This rare but severe deficiency is an autosomal recessive trait, which usually results in early childhood death as there is currently no available treatment.^[4][5][6][7]