Kinetic, Inhibition, and Structural Characterization of a Malonate Semialdehyde Decarboxylase-like Protein from Calothrix sp. PCC 6303: A Gateway to the non-Pro1 Tautomerase Superfamily Members.
Kinetic, Inhibition, and Structural Characterization of a Malonate Semialdehyde Decarboxylase-like Protein from Calothrix sp. PCC 6303: A Gateway to the non-Pro1 Tautomerase Superfamily Members.
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DOI：
10.1021/acs.biochem.2c00101
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发表时间：
2022-05-13
期刊：
影响因子：
2.9
通讯作者：
Whitman, Christian P.
中科院分区：
文献类型：
--
作者：
Lancaster, Emily B.;Yang, Wanjie;Johnson, William H., Jr.;Baas, Bert-Jan;Zhang, Yan Jessie;Whitman, Christian P.
长期以来，氨基末端脯氨酸 (Pro1) 一直被认为是互变异构酶超家族 (TSF) 酶的机械必需品，在所有特征反应中充当通用碱或酸。然而，对 TSF 11,000 多个非冗余序列的全面检查发现了 346 个缺乏 Pro1 的序列。大多数 (~85%) 存在于丙二酸半醛脱羧酶 (MSAD) 亚组中，其中 294 个序列中的大多数形成一个单独的簇。该簇内的四个序列保留 Pro1。因为这四个序列可能提供线索来帮助识别和表征附近没有 Pro1 的序列的活性，所以通过动力学、抑制和晶体学研究对它们进行了检查。四种中最有前途的一种（来自 Calothrix sp. PCC 6303，指定为 437）表现出脱羧酶和互变异构酶活性，并在 Pro1 处被 3-溴丙炔酸共价修饰。获得了 apo 酶的晶体结构（2.35 Å 分辨率）。与 Pro1 形成 3-氧代丙酸酯加合物为构建结合配体的分子模型提供了线索。建模的配体延伸到允许与三个残基（Lys37、Arg56、Glu98）相互作用的区域，表明这些残基可能在观察到的脱羧和互变异构活性中发挥作用。此外，这些相同的残基在序列相似性网络中的 16 个附近的非 Pro1 序列中是保守的。到目前为止，这些残基尚未涉及任何其他 TSF 成员的机制。收集的观察结果为非 Pro1 序列的表征提供了起点。
The amino-terminal proline (Pro1) has long been thought to be a mechanistic imperative for tautomerase superfamily (TSF) enzymes, functioning as a general base or acid in all characterized reactions. However, a global examination of more than 11,000 nonredundant sequences of the TSF uncovered 346 sequences that lack Pro1. The majority (~85%) are found in the malonate semialdehyde decarboxylase (MSAD) subgroup where most of the 294 sequences form a separate cluster. Four sequences within this cluster retain Pro1. Because these four sequences might provide clues to assist in the identification and characterization of activities of nearby sequences without Pro1, they were examined by kinetic, inhibition, and crystallographic studies. The most promising of the four (from Calothrix sp. PCC 6303 designated 437) exhibited decarboxylase and tautomerase activities and was covalently modified at Pro1 by 3-bromopropiolate. A crystal structure was obtained for the apo enzyme (2.35 Å resolution). The formation of a 3-oxopropanoate adduct with Pro1 provides clues to build a molecular model for the bound ligand. The modeled ligand extends into a region that allows interactions with three residues (Lys37, Arg56, Glu98), suggesting that these residues could play roles in the observed decarboxylation and tautomerization activities. Moreover, these same residues are conserved in 16 nearby, non-Pro1 sequences in a sequence similarity network. Thus far, these residues have not been implicated in the mechanisms of any other TSF members. The collected observations provide starting points for the characterization of the non-Pro1 sequences.
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DOI：
10.1074/jbc.m117.815340
发表时间：
2018-02-16
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Davidson R;Baas BJ;Akiva E;Holliday GL;Polacco BJ;LeVieux JA;Pullara CR;Zhang YJ;Whitman CP;Babbitt PC
通讯作者：
Babbitt PC
影响因子：
2.9
作者：
Burks, Elizabeth A.;Fleming, Christopher D.;Mesecar, Andrew D.;Whitman, Christian P.;Pegan, Scott D.
通讯作者：
Pegan, Scott D.
DOI：
10.1073/pnas.69.12.3506
发表时间：
1972-01-01
影响因子：
11.1
作者：
HOUMARD, J;DRAPEAU, GR
通讯作者：
DRAPEAU, GR
影响因子：
2.9
作者：
Guo, Youzhong;Serrano, Hector;Poelarends, Gerrit J.;Johnson, William H., Jr.;Hackert, Marvin L.;Whitman, Christian P.
通讯作者：
Whitman, Christian P.
影响因子：
2.9
作者：
Almrud, JJ;Poelarends, GJ;Whitman, CP
通讯作者：
Whitman, CP