Ge Jie, Yu Guixue, Ator Mark A, Stubbe JoAnne
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
Biochemistry. 2003 Sep 2;42(34):10071-83. doi: 10.1021/bi034374r.
E. coli ribonucleotide reductase (RNR) catalyzes the conversion of nucleoside diphosphates (NDPs) to dNDPs and is composed of two homodimeric subunits: R1 and R2. R1 binds NDPs and contains binding sites for allosteric effectors that control substrate specificity and turnover rate. R2 contains a diiron-tyrosyl radical (Y()) cofactor that initiates nucleotide reduction. Pre-steady-state experiments with wild type R1 or C754S/C759S-R1 and R2 were carried out to determine which step(s) are rate-limiting and whether both active sites of R1 can catalyze nucleotide reduction. Rapid chemical quench experiments monitoring dCDP formation gave k(obs) of 9 +/- 4 s(-1) with an amplitude of 1.7 +/- 0.4 equiv. This amplitude, generated in experiments with pre-reduced R1 (3 or 15 microM) in the absence of reductant, indicates that both monomers of R1 are active. Stopped-flow UV-vis spectroscopy monitoring the concentration of the Y() failed to reveal any changes from 2 ms to seconds under similar conditions. These pre-steady-state experiments, in conjunction with the steady-state turnover numbers for dCDP formation of 2-14 s(-1) at RNR concentrations of 0.05-0.4 microM (typical assay conditions), reveal that the rate-determining step is a physical step prior to rapid nucleotide reduction and rapid tyrosine reoxidation to Y(*). Steady-state experiments conducted at RNR concentrations of 3 and 15 microM, typical of pre-steady-state conditions, suggest that, in addition to the slow conformational change(s) prior to chemistry, re-reduction of the active site disulfide to dithiol or a conformational change accompanying this process can also be rate-limiting.
大肠杆菌核糖核苷酸还原酶(RNR)催化核苷二磷酸(NDPs)转化为脱氧核苷二磷酸(dNDPs),它由两个同型二聚体亚基组成:R1和R2。R1结合NDPs,并含有用于控制底物特异性和周转率的变构效应物的结合位点。R2含有一个双铁 - 酪氨酸自由基(Y())辅因子,该辅因子启动核苷酸还原。使用野生型R1或C754S/C759S - R1与R2进行了预稳态实验,以确定哪些步骤是限速步骤,以及R1的两个活性位点是否都能催化核苷酸还原。监测dCDP形成的快速化学淬灭实验得出k(obs)为9±4 s(-1),幅度为1.7±0.4当量。在没有还原剂的情况下,用预还原的R1(3或15 microM)进行实验产生的这个幅度表明R1的两个单体都是有活性的。在类似条件下,通过停流紫外 - 可见光谱监测Y()的浓度,从2毫秒到数秒都未发现任何变化。这些预稳态实验,结合在RNR浓度为0.05 - 0.4 microM(典型测定条件)下dCDP形成的稳态周转数为2 - 14 s(-1),表明限速步骤是在快速核苷酸还原和酪氨酸快速再氧化为Y(*)之前的一个物理步骤。在RNR浓度为3和15 microM(典型的预稳态条件)下进行的稳态实验表明,除了化学作用之前的缓慢构象变化外,活性位点二硫键再还原为二硫醇或伴随此过程的构象变化也可能是限速的。