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Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control.

Chitnumsub P, Jaruwat A, Riangrungroj P, Ittarat W, Noytanom K, Oonanant W, Vanichthanankul J, Chuankhayan P, Maenpuen S, Chen CJ, Chaiyen P, Yuthavong Y, Leartsakulpanich U - Acta Crystallogr. D Biol. Crystallogr. (2014)

Bottom Line: Likewise, a large surface area with a highly positively charged electrostatic potential surrounding the PvSHMT folate pocket suggested a preference for a polyglutamated folate substrate similar to the mammalian SHMTs.Furthermore, as in P. falciparum SHMT, a redox switch created from a cysteine pair (Cys125-Cys364) was observed.Overall, these results assert the importance of features such as stereoselectivity and redox status for control of the activity and specificity of PvSHMT.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand.

ABSTRACT
Plasmodium parasites, the causative agent of malaria, rely heavily on de novo folate biosynthesis, and the enzymes in this pathway have therefore been explored extensively for antimalarial development. Serine hydroxymethyltransferase (SHMT) from Plasmodium spp., an enzyme involved in folate recycling and dTMP synthesis, has been shown to catalyze the conversion of L- and D-serine to glycine (Gly) in a THF-dependent reaction, the mechanism of which is not yet fully understood. Here, the crystal structures of P. vivax SHMT (PvSHMT) in a binary complex with L-serine and in a ternary complex with D-serine (D-Ser) and (6R)-5-formyltetrahydrofolate (5FTHF) provide clues to the mechanism underlying the control of enzyme activity. 5FTHF in the ternary-complex structure was found in the 6R form, thus differing from the previously reported structures of SHMT-Gly-(6S)-5FTHF from other organisms. This suggested that the presence of D-Ser in the active site can alter the folate-binding specificity. Investigation of binding in the presence of D-Ser and the (6R)- or (6S)-5FTHF enantiomers indicated that both forms of 5FTHF can bind to the enzyme but that only (6S)-5FTHF gives rise to a quinonoid intermediate. Likewise, a large surface area with a highly positively charged electrostatic potential surrounding the PvSHMT folate pocket suggested a preference for a polyglutamated folate substrate similar to the mammalian SHMTs. Furthermore, as in P. falciparum SHMT, a redox switch created from a cysteine pair (Cys125-Cys364) was observed. Overall, these results assert the importance of features such as stereoselectivity and redox status for control of the activity and specificity of PvSHMT.

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Surface electrostatic potential. (a) Dimeric PvSHMT–d-Ser–(6R)-5FTHF, with the inset showing key residues involved in folate binding: Tyr′54, Glu′56, Lys′60, Lys′61, Tyr′63 and Tyr′64 in the YEY loop and Lys138 and Lys139 in loop-C125. (b) Dimeric ecSHMT (PDB entry 1dfo). (c) Tetrameric rSHMT (PDB entry 1ls3). Each structure contains 5FTHF, but that of rSHMT contains triGlu-5FTHF.
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fig5: Surface electrostatic potential. (a) Dimeric PvSHMT–d-Ser–(6R)-5FTHF, with the inset showing key residues involved in folate binding: Tyr′54, Glu′56, Lys′60, Lys′61, Tyr′63 and Tyr′64 in the YEY loop and Lys138 and Lys139 in loop-C125. (b) Dimeric ecSHMT (PDB entry 1dfo). (c) Tetrameric rSHMT (PDB entry 1ls3). Each structure contains 5FTHF, but that of rSHMT contains triGlu-5FTHF.

Mentions: Another difference lies in the SHMT architecture and the electrostatic potential. The surface of mammalian and Plasmodium SHMTs is positively charged near the folate glutamate moiety, while that of bacterial SHMTs is negatively charged (Fig. 5 ▶). Additionally, positively charged residues, namely Lys138 and Lys139 on loop-C125Pv and Lys′60 and Lys′61 on the YEY loop of the second protomer, are located on the surface of the THF-binding pocket (Fig. 5 ▶a). It is likely that these residues contribute to the binding affinity of poly-γ-­glutamate–THF.


Structures of Plasmodium vivax serine hydroxymethyltransferase: implications for ligand-binding specificity and functional control.

Chitnumsub P, Jaruwat A, Riangrungroj P, Ittarat W, Noytanom K, Oonanant W, Vanichthanankul J, Chuankhayan P, Maenpuen S, Chen CJ, Chaiyen P, Yuthavong Y, Leartsakulpanich U - Acta Crystallogr. D Biol. Crystallogr. (2014)

Surface electrostatic potential. (a) Dimeric PvSHMT–d-Ser–(6R)-5FTHF, with the inset showing key residues involved in folate binding: Tyr′54, Glu′56, Lys′60, Lys′61, Tyr′63 and Tyr′64 in the YEY loop and Lys138 and Lys139 in loop-C125. (b) Dimeric ecSHMT (PDB entry 1dfo). (c) Tetrameric rSHMT (PDB entry 1ls3). Each structure contains 5FTHF, but that of rSHMT contains triGlu-5FTHF.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257618&req=5

fig5: Surface electrostatic potential. (a) Dimeric PvSHMT–d-Ser–(6R)-5FTHF, with the inset showing key residues involved in folate binding: Tyr′54, Glu′56, Lys′60, Lys′61, Tyr′63 and Tyr′64 in the YEY loop and Lys138 and Lys139 in loop-C125. (b) Dimeric ecSHMT (PDB entry 1dfo). (c) Tetrameric rSHMT (PDB entry 1ls3). Each structure contains 5FTHF, but that of rSHMT contains triGlu-5FTHF.
Mentions: Another difference lies in the SHMT architecture and the electrostatic potential. The surface of mammalian and Plasmodium SHMTs is positively charged near the folate glutamate moiety, while that of bacterial SHMTs is negatively charged (Fig. 5 ▶). Additionally, positively charged residues, namely Lys138 and Lys139 on loop-C125Pv and Lys′60 and Lys′61 on the YEY loop of the second protomer, are located on the surface of the THF-binding pocket (Fig. 5 ▶a). It is likely that these residues contribute to the binding affinity of poly-γ-­glutamate–THF.

Bottom Line: Likewise, a large surface area with a highly positively charged electrostatic potential surrounding the PvSHMT folate pocket suggested a preference for a polyglutamated folate substrate similar to the mammalian SHMTs.Furthermore, as in P. falciparum SHMT, a redox switch created from a cysteine pair (Cys125-Cys364) was observed.Overall, these results assert the importance of features such as stereoselectivity and redox status for control of the activity and specificity of PvSHMT.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Klong Nueng, Klong Luang, Pathum Thani 12120, Thailand.

ABSTRACT
Plasmodium parasites, the causative agent of malaria, rely heavily on de novo folate biosynthesis, and the enzymes in this pathway have therefore been explored extensively for antimalarial development. Serine hydroxymethyltransferase (SHMT) from Plasmodium spp., an enzyme involved in folate recycling and dTMP synthesis, has been shown to catalyze the conversion of L- and D-serine to glycine (Gly) in a THF-dependent reaction, the mechanism of which is not yet fully understood. Here, the crystal structures of P. vivax SHMT (PvSHMT) in a binary complex with L-serine and in a ternary complex with D-serine (D-Ser) and (6R)-5-formyltetrahydrofolate (5FTHF) provide clues to the mechanism underlying the control of enzyme activity. 5FTHF in the ternary-complex structure was found in the 6R form, thus differing from the previously reported structures of SHMT-Gly-(6S)-5FTHF from other organisms. This suggested that the presence of D-Ser in the active site can alter the folate-binding specificity. Investigation of binding in the presence of D-Ser and the (6R)- or (6S)-5FTHF enantiomers indicated that both forms of 5FTHF can bind to the enzyme but that only (6S)-5FTHF gives rise to a quinonoid intermediate. Likewise, a large surface area with a highly positively charged electrostatic potential surrounding the PvSHMT folate pocket suggested a preference for a polyglutamated folate substrate similar to the mammalian SHMTs. Furthermore, as in P. falciparum SHMT, a redox switch created from a cysteine pair (Cys125-Cys364) was observed. Overall, these results assert the importance of features such as stereoselectivity and redox status for control of the activity and specificity of PvSHMT.

Show MeSH
Related in: MedlinePlus