Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain.
Phylogenetic and amino acid conservation analyses of bacterial L-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain.
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DOI：
10.1186/s13104-015-1314-6
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发表时间：
2015-08-15
影响因子：
1.8
通讯作者：
Escalante-Semerena JC
中科院分区：
文献类型：
--
作者：
Stuecker TN;Bramhacharya S;Hodge-Hanson KM;Suen G;Escalante-Semerena JC
所有生物体都必须从前体泛酸合成酶辅助因子辅酶 A (CoA)。大多数细菌可以通过泛解酸和β-丙氨酸的缩合从头合成泛酸。 β-丙氨酸的合成由 L-天冬氨酸-α-脱羧酶 (PanD) 催化，这是一种最初作为酶原 (pro-PanD) 合成的丙酮酰酶。活性 PanD 是通过 pro-PanD 在 Gly24-Ser25 处自裂解产生活性位点丙酮酰基部分。在肠沙门氏菌中，这种裂解需要 PanM，一种与 Gcn5 样 N-乙酰转移酶相关的乙酰辅酶 A 传感器。 PanM 不会乙酰化 pro-PanD，但最近发表的 PanM 同源物 PanZ 与大肠杆菌 PanD 酶原复合物的三维晶体结构验证了我们的预测，并提供了进一步研究裂解机制的框架。相比之下，来自缺乏 PanM 的细菌的 PanD 在体内缺乏 PanM 的情况下可有效裂解。通过系统发育分析结合体内表型研究，我们发现存在两类细菌 L-天冬氨酸-α-脱羧酶。这种分类是基于它们通过酶原的自我裂解而进行的翻译后激活。 I 类 l-天冬氨酸-α-脱羧酶酶原需要乙酰辅酶 A 传感器 PanM 裂解成活性 PanD。该类仅存在于伽马变形菌门中。 II 类 l-天冬氨酸-α-脱羧酶酶原在 PanM 不存在的情况下可有效地自裂解，并且存在于多种细菌门中。广古菌门和泉古菌门的一些成员也含有 II 类 l-天冬氨酸-α-脱羧酶。 PanM 的系统发育和氨基酸保守分析揭示了 PanM 的保守区域与相关 Gcn5 相关乙酰转移酶 (Pfam00583) 中发现的保守区域不同。该保守区域代表与 L-天冬氨酸-α-脱羧酶酶原相互作用的推定结构域。这项工作可能为未来 pro-PanD-PanM 相互作用的生化和结构研究提供信息。实验结果表明，肠沙门氏菌和谷氨酸棒杆菌-天冬氨酸-α-脱羧酶代表了这些酶的两类不同的同源物。 I 类同系物需要 PanM 才能激活，而 II 类同系物在没有 PanM 的情况下会自我裂解。使用蛋白质数据库 (RCSB PDB) 中提供的 PanM 和 l-天冬氨酸-α-脱羧酶的结构坐标对保守氨基酸进行计算机建模，揭示了假定的相互作用位点，这可能有助于生成模型，以帮助理解 l-天冬氨酸-α-脱羧酶自裂解机制的分子细节。本文的在线版本 (doi:10.1186/s13104-015-1314-6) 包含补充材料，可供授权用户使用。
All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by l-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the active-site pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo. Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial l-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I l-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II l-aspartate-α-decarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II l-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with l-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions. Experimental results indicate that S. enterica and C. glutamicuml-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and l-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of l-aspartate-α-decarboxylases. The online version of this article (doi:10.1186/s13104-015-1314-6) contains supplementary material, which is available to authorized users.