The long-term goal of the project is to determine the structures and molecular mechanisms of catalysis for enzymes in the folate biosynthetic pathway, a proven target pathway for developing antimicrobial agents. The proposed research is to continue our current study on 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), and to expand our research to include dihydroneopterin aldolase (DHNA). HPPK is an excellent model for studying mechanism of enzymatic pyrophosphoryl transfer. DHNA is a unique aldolase because it requires neither the formation of a Schiff base between the enzyme and its substrate nor metal ions for catalysis, and the enzyme also catalyzes the epimerization of its substrate. The central hypothesis behind the proposed research on HPPK, which is based on the results obtained in the previous funding period, is that HPPK undergoes dramatic conformational changes during its catalytic cycle and the conformational changes play critical roles in its catalysis. Thus, in Specific Aim 1, we will continue our quest for structure determination of HPPK along the catalytic cycle by X-ray crystallography.
In Specific Aim 2, we will determine the conformational dynamics of the catalytic loops of HPPK by time-resolved fluorescence energy transfer (FRET) at equilibrium conditions and even as the reaction progresses and the dynamics of its core structure by heteronuclear NMR relaxation at the sub-nanosecond to nanosecond and microsecond to millisecond time scales. Most importantly, in Specific Aim 3, we will correlate the structure and conformational dynamics of HPPK with its catalysis by site-directed mutagenesis, biochemical analysis (particularly transient kinetic analysis), and biophysical methods. The main hypotheses behind the proposed research on DHNA are that (1) the two adlolases from Staphylococcus aureus and E. coil have different binding/catalytic properties and distinct responses to inhibitors and (2) general acid/base catalysis plays a most critical role in the catalytic mechanism of this unique aldolase. Thus, in Specific Aim 4, we will determine the structures of DHNA by X-ray crystallography, particularly the structures of the complexes with neopterin and monopterin, the closest mimics of the Michaelis complexes of DHNA.
In Specific Aim 5, we will identify residues involved in general acid/base catalysis in DHNA by a combination of site-directed mutagenesis, transient kinetic pH-rate profile analysis, and NMR spectroscopic titration.
|Achila, David; Liu, Aizhuo; Banerjee, Rahul et al. (2015) Structural determinants of host specificity of complement Factor H recruitment by Streptococcus pneumoniae. Biochem J 465:325-35|
|Shaw, Gary X; Li, Yue; Shi, Genbin et al. (2014) Structural enzymology and inhibition of the bi-functional folate pathway enzyme HPPK-DHPS from the biowarfare agent Francisella tularensis. FEBS J 281:4123-37|
|Chen, Bin; Himes, Paul; Liu, Yu et al. (2014) Structure of bacterial transcription factor SpoIIID and evidence for a novel mode of DNA binding. J Bacteriol 196:2131-42|
|Wang, Jifeng; Sklenak, Stepan; Liu, Aizhuo et al. (2012) Role of glutamate 64 in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminase. Biochemistry 51:475-86|
|He, Yufan; Li, Yue; Mukherjee, Saptarshi et al. (2011) Probing single-molecule enzyme active-site conformational state intermittent coherence. J Am Chem Soc 133:14389-95|
|Lescop, Ewen; Lu, Zhenwei; Liu, Qin et al. (2009) Dynamics of the conformational transitions in the assembling of the Michaelis complex of a bisubstrate enzyme: a (15)N relaxation study of Escherichia coli 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase. Biochemistry 48:302-12|
|Liu, Aizhuo; Wang, Jifeng; Lu, Zhenwei et al. (2008) Hydrogen-bond detection, configuration assignment and rotamer correction of side-chain amides in large proteins by NMR spectroscopy through protium/deuterium isotope effects. Chembiochem 9:2860-71|
|Liu, Aizhuo; Lu, Zhenwei; Wang, Jifeng et al. (2008) NMR detection of bifurcated hydrogen bonds in large proteins. J Am Chem Soc 130:2428-9|
|Yao, Lishan; Yan, Honggao; Cukier, Robert I (2007) A molecular dynamics study of the ligand release path in yeast cytosine deaminase. Biophys J 92:2301-10|
|Liu, Aizhuo; Yao, Lishan; Li, Yue et al. (2007) TROSY of side-chain amides in large proteins. J Magn Reson 186:319-26|
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