Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.
Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes.
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在类异丙生素生物合成酶中保守的天冬酰胺，谷氨酰胺，丝氨酸和酪氨酸残基的催化作用。
DOI：
10.1021/acscatal.8b00543
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发表时间：
2018-05-04
期刊：
影响因子：
12.9
通讯作者：
Guo RT
中科院分区：
文献类型：
--
作者：
Malwal SR;Gao J;Hu X;Yang Y;Liu W;Huang JW;Ko TP;Li L;Chen CC;O'Dowd B;Khade RL;Zhang Y;Zhang Y;Oldfield E;Guo RT
我们报告的结果调查的催化作用的高度保守的酰胺（天冬酰胺，谷氨酰胺）和OH-含（丝氨酸，酪氨酸）残基在几个异戊二烯转移酶。我们首次获得了含有两个分子的底物类似物二甲基烯丙基（S）-硫代二磷酸（DMASPP）的cyclolavandulyl二磷酸合酶的X射线结构。这两个分子具有类似的二磷酸基团的方向，在其他的α-折叠（顺式-头-尾和头-中）异戊二烯基转移酶，具有一个二磷酸部分，在所谓的S1位点与Mg 2+形成二齿螯合物（其通常是β-折叠蛋白中的烯丙基结合位点），而第二个二磷酸在所谓的S2位点与Mg 2+结合（其通常是β-折叠蛋白中的高烯丙基结合位点）通过单个P1 O 1氧。后一种相互作用可以促进通过P1 O2的直接磷酸盐介导的质子提取，或者更可能通过间接机制，其中P1 O2稳定碱性天冬酰胺物质，其去除H+，然后通过Asn-Ser穿梭消除。Asn-Ser对在β-折叠蛋白中的普遍存在导致了这样的想法，即在许多“头对头”异戊烯基转移酶如角鲨烯和脱氢角鲨烯合酶中看到的高度保守的酰胺（Asn，Gln）和含OH（Tyr）残基可能在H+消除中发挥类似的作用。结构，生物信息学和诱变研究确实表明这些残基在催化中的重要作用，与密度泛函理论计算的结果表明，Asn绑定到Mg 2+可以作为一个通用的（亚胺样）基地，而谷氨酰胺，酪氨酸和H2O形成一个质子通道，是相邻的常规（天冬氨酸丰富）的“活性位点”。两者合计，我们的研究结果导致质子消除从碳阳离子在许多异戊烯基转移酶中的中性物种（天冬酰胺，谷氨酰胺，丝氨酸，酪氨酸，水）作为质子穿梭机的机制，补充了更熟悉的作用，酸性基团（在天冬氨酸和谷氨酸），结合到Mg 2+，和碱性基团（主要是精氨酸），结合到二磷酸盐，在类异戊二烯生物合成。在催化类异戊二烯生物合成的蛋白质中，高度保守的含酰胺和羟基的氨基酸残基参与质子消除
We report the results of an investigation into the catalytic role of highly conserved amide (asparagine, glutamine) and OH-containing (serine, tyrosine) residues in several prenyltransferases. We first obtained the X-ray structure of cyclolavandulyl diphosphate synthase containing two molecules of the substrate analog dimethylallyl (S)-thiolodiphosphate (DMASPP). The two molecules have similar diphosphate group orientations to those seen in other ζ-fold (cis- head-to-tail and head-to-middle) prenyltransferases with one diphosphate moiety forming a bidentate chelate with Mg2+ in the so-called S1 site (which is typically the allylic binding site in ζ-fold proteins) while the second diphosphate binds to Mg2+ in the so-called S2 site (which is typically the homoallylic binding site in ζ-fold proteins) via a single P1O1 oxygen. The latter interaction can facilitate direct phosphate-mediated proton abstraction via P1O2, or more likely by an indirect mechanism in which P1O2 stabilizes a basic asparagine species that removes H+, which is then eliminated via an Asn-Ser shuttle. The universal occurrence of Asn-Ser pairs in ζ-fold proteins leads to the idea that the highly conserved amide (Asn, Gln) and OH-containing (Tyr) residues seen in many “head-to-head” prenyltransferases such as squalene and dehydrosqualene synthase might play similar roles, in H+ elimination. Structural, bioinformatics and mutagenesis investigations indeed indicate an important role of these residues in catalysis, with the results of density functional theory calculations showing that Asn bound to Mg2+ can act as a general (imine-like) base, while Gln, Tyr and H2O form a proton channel that is adjacent to the conventional (Asp-rich) “active site”. Taken together, our results lead to mechanisms of proton-elimination from carbocations in numerous prenyltransferases in which neutral species (Asn, Gln, Ser, Tyr, H2O) act as proton shuttles, complementing the more familiar roles of acidic groups (in Asp and Glu) that bind to Mg2+, and basic groups (primarily Arg) that bind to diphosphates, in isoprenoid biosynthesis. Highly conserved amide and hydroxy-containing amino-acid residues are involved in proton elimination in proteins catalyzing isoprenoid biosynthesis
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影响因子：
16.6
作者：
Oldfield, Eric;Lin, Fu-Yang
通讯作者：
Lin, Fu-Yang
DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
4.8
作者：
Gu, PD;Ishii, Y;Shechter, I
通讯作者：
Shechter, I
病原细菌中的头对头异戊二烯合成酶
DOI：
10.1002/cbic.201700099
发表时间：
2017-06-01
期刊：
Chembiochem : a European journal of chemical biology
影响因子：
--
作者：
Schwalen CJ;Feng X;Liu W;O-Dowd B;Ko TP;Shin CJ;Guo RT;Mitchell DA;Oldfield E
通讯作者：
Oldfield E
DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH