Strader Michael Brad, Chopra Shaileja, Jackson Michael, Smiley R Derike, Stinnett Lori, Wu Jun, Howell Elizabeth E
Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-0840, USA.
Biochemistry. 2004 Jun 15;43(23):7403-12. doi: 10.1021/bi049646k.
R67 dihydrofolate reductase (DHFR) is a novel protein that possesses 222 symmetry. A single active site pore traverses the length of the homotetramer. Although the 222 symmetry implies that four symmetry-related binding sites should exist for each substrate as well as each cofactor, isothermal titration calorimetry (ITC) studies indicate only two molecules bind. Three possible combinations include two dihydrofolate molecules, two NADPH molecules, or one substrate with one cofactor. The latter is the productive ternary complex. To evaluate the roles of A36, Y46, T51, G64, and V66 residues in binding and catalysis, a site-directed mutagenesis approach was employed. One mutation per gene produces four mutations per active site pore, which often result in large cumulative effects. Conservative mutations at these positions either eliminate the ability of the gene to confer trimethoprim resistance or have no effect on catalysis. This result, in conjunction with previous mutagenesis studies on K32, K33, S65, Q67, I68, and Y69 [Strader, M. B., et al. (2001) Biochemistry 40, 11344-11352; Hicks, S. N., et al. (2003) Biochemistry 42, 10569-10578; Park, H., et al. (1997) Protein Eng. 10, 1415-1424], allows mapping of the active site surface. Residues for which conservative mutations have large effects on binding and catalysis include K32, Q67, I68, and Y69. These residues form a stripe that establishes the ligand binding surface. Residues that accommodate conservative mutations that do not greatly affect catalysis include K33, Y46, T51, S65, and V66. Isothermal titration calorimetry studies were also conducted on many of the mutants described above to determine the enthalpy of folate binding to the R67 DHFR.NADPH complex. A linear correlation between this DeltaH value and log k(cat)/K(m) is observed. Since structural tightness appears to be correlated with the exothermicity of the binding interaction, this leads to the hypothesis that enthalpy-driven formation of the ternary complex in these R67 DHFR variants plays a strong role in catalysis. Use of the alternate cofactor, NADH, extends this correlation, indicating preorganization of the ternary complex determines the efficiency of the reaction. This hypothesis is consistent with data suggesting R67 DHFR uses an endo transition state (where the nicotinamide ring of cofactor overlaps the more bulky side of the substrate's pteridine ring).
R67二氢叶酸还原酶(DHFR)是一种具有222对称性的新型蛋白质。一个单一的活性位点孔贯穿同四聚体的长度。尽管222对称性意味着每个底物以及每个辅因子应该存在四个对称相关的结合位点,但等温滴定量热法(ITC)研究表明只有两个分子结合。三种可能的组合包括两个二氢叶酸分子、两个NADPH分子,或一个底物与一个辅因子。后者是有活性的三元复合物。为了评估A36、Y46、T51、G64和V66残基在结合和催化中的作用,采用了定点诱变方法。每个基因一个突变在每个活性位点孔中产生四个突变,这通常会导致较大的累积效应。这些位置的保守突变要么消除基因赋予甲氧苄啶抗性的能力,要么对催化没有影响。这个结果,结合先前对K32、K33、S65、Q67、I68和Y69的诱变研究[斯特拉德,M.B.等人(2001年)《生物化学》40,11344 - 11352;希克斯,S.N.等人(2003年)《生物化学》42,10569 - 10578;朴,H.等人(1997年)《蛋白质工程》10,1415 - 1424],允许绘制活性位点表面。保守突变对结合和催化有很大影响的残基包括K32、Q67、I68和Y69。这些残基形成一条带,确定了配体结合表面。容纳对催化影响不大的保守突变的残基包括K33、Y46、T51、S65和V66。还对上述许多突变体进行了等温滴定量热法研究,以确定叶酸与R67 DHFR·NADPH复合物结合的焓。观察到该ΔH值与log k(cat)/K(m)之间存在线性相关性。由于结构紧密性似乎与结合相互作用的放热性相关,这导致了这样的假设,即在这些R67 DHFR变体中,三元复合物的焓驱动形成在催化中起重要作用。使用替代辅因子NADH扩展了这种相关性,表明三元复合物的预组织决定了反应效率。这个假设与表明R67 DHFR使用内过渡态(其中辅因子的烟酰胺环与底物蝶啶环较大的一侧重叠)的数据一致。