In Plasmodium parasites, pyrimidine nucleotides are synthesized de novo
via a six-step pathway1.
One of the steps involves addition of a ribosyl phosphate group
to orotic acid by orotate phosphoribosyltransferase (OPRT),
resulting to orotidine 5'-monophosphate (OMP).
Subsequently, orotidine 5'-monophosphate decarboxylase (OMPDC)
catalyses the removal of the carboxyl group from OMP to produce,
uridine monophosphate (UMP),
from which all pyrimidine nucleotides can be derived.
This decarboxylation step is accelerated by a factor of 1017
without the benefit of a catalytic cofactor by OMPDC,
making it the most efficient of all enzymes.2
Despite the availability of the structures of OMPDC in other organisms
(e.g. E. coli - 1EIX,
M. thermoautotrophicum - 1DV7,
B. subtilis - 1DBT,
S. cerevisiae - 1DQW)
in apo form and in complexes with UMP and its analogs,
including 6-hydroxyuridine 5'-monophosphate (BMP) and 6-azauridine 5'-monophosphate,3
the mechanism of decarboxylation of OMP to UMP remains uncertain.
We have solved the native structure of orotidine 5-monophosphate decarboxylase from
Plasmodium yoelii
PY01515,
Plasmodium berghei
NCBI accession XP_679107
and Plasmodium vivax
TIGR accession Pv111555.
All orthologs feature the signature DxKxxDIxxT motif in their catalytic sites
(DMKINDIGNT in both cases).
As shown below, the is strong sequence homology amongst the Plasmodium family of OMPDC,
even though each is only about 20% identical to the same enzyme in other organisms.
The P. berghei and P. yoelii enzymes are 85% identical,
with both being 68% identical to the Pf OMPDC
and about 50% identical to the P. vivax orthologue.
The orthologues from the human parasites, namely Pf and Pv,
are 62% identical.
As with other proteins, OMPDC from P. knowlesi is 82% identical to
the P. vivax enzyme and 62% identical to the P. falciparum orthologue.
PBG-PF10_0225 -HFKTKLKNRRNEVNTCLCIGLDPDEDDIKNFMRNEEKNGYKNVKNNMNSNNNRI-----------ENVIKIGKEILLTDEENIENLSEE
PY01515 MHFKTKLKNRRSEVNTCLCIGLDPDEDDIKNFMKNEEQNGYKNIKNNMNSNNNGI-----------ENIIKIGKEILLTDGENIQNLSEE
PF10_0225 MGFKVKLEKRRNAINTCLCIGLDPDEKDIENFMKNEKENNYNNIKKNLKEKY--------------INNVSIKKDILLKAPDNIIREEKS
PKN-PF10_0225 MNLKTKLQKRRDEVNTCLCIGLDPDEADIKSFMQSEKQNGYQSIKKNLSNHGSSS--------QGGLFTPQVGGTMLLAENPPKE-VQEK
PV-PF10_0225 -NLKIKLQKRRDEVNTCLCIGLDPDEADIKSFMQSEKQNGYQSVKKNLSNSGSSSSSSNSSSGKGELFAPQMGGQMLLAETPPKE-AQEK
PBG-PF10_0225 DKFFYFFNHFCFYIINNTKEYALIYKMNFAFYIPYGSVGINALKNVFDYLNSMNIPTMLDMKINDIGNTVKNYRKFIFEYLKSDSCTINV
PY01515 DKFFYFFNHFCFYIINNTKEYALVYKMNFAFYIPYGSVGINALKNVFDYLNSMNIPTMLDMKINDIGNTVKNYRKFIFEYLKSDSCTINV
PF10_0225 EEFFYFFNHFCFYIINETNKYALTFKMNFAFYIPYGSVGIDVLKNVFDYLYELNIPTILDMKINDIGNTVKNYRKFIFEYLKSDSCTVNI
PKN-PF10_0225 DEFFYFFNHFCFYIINETKQYALSYKMNFAFYLPYGSLGVDVLKNVFDYLHYLDVPTILDIKMNDIGNTVKHYS