The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
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DOI：
10.1186/1471-2105-6-172
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发表时间：
2005-07-12
影响因子：
3
通讯作者：
Bujnicki JM
中科院分区：
文献类型：
--
作者：
Kosinski J;Feder M;Bujnicki JM
PD-(D/E)XK 核酸酶超家族最初在 II 型限制性内切酶中发现，后来在许多涉及 DNA 重组和修复的酶中发现，是蛋白质序列分析和结构预测中最具挑战性的靶标之一。通常，这些蛋白质之间的序列相似性非常低，以至于 PD-(D/E)XK 超家族已知成员之间的大多数关系只有在通过实验确定相应结构后才能确定。因此，人们很容易推测，在未表征的蛋白质家族中，还有潜在的核酸酶有待发现，但它们的识别需要比传统 PSI-BLAST 搜索更灵敏的工具。氨基酸保守程度低阻碍了仅根据与已知成员的序列比较来鉴定 PD-(D/E)XK 超家族新成员的可能性。因此，我们使用最近开发的方法 HHsearch 来灵敏地检测蛋白质家族之间的远程相似性，这些蛋白质家族表示为通过二级结构增强的轮廓隐藏马尔可夫模型。我们将已知的 PD-(D/E)XK 核酸酶家族与数据库进行了比较，该数据库包含对应于功能表征和未表征的蛋白质家族的 COG 和 PFAM 图谱，以检测显着的相似性。随后通过序列结构线索、比较建模和潜在活性位点残基的鉴定来验证新核酸酶的初始候选物。在本文中，我们报告了在与 DNA 相互作用有关但结构和作用机制未知的许多蛋白质（例如推定的重组酶 RmuC、DNA 能力因子 CoiA、DNA 结合蛋白 SfsA、预测为 DNA 修复酶的大型人类蛋白质、预测的古菌转录调节因子和噬菌体 T4 的头部完成蛋白）以及迄今为止尚未指定功能的蛋白质（例如YhcG，各种噬菌体蛋白，限制性内切酶的新候选者）。我们的结果有助于减少蛋白质宇宙序列-结构-功能图上的“空白”，并将有助于启动新核酸酶的实验表征，其中许多核酸酶对于全面理解控制基因组进化和稳定性的机制可能具有重要意义。
The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. Typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the PD-(D/E)XK superfamily were identified only after the corresponding structures were determined experimentally. Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches. The low degree of amino acid conservation hampers the possibility of identification of new members of the PD-(D/E)XK superfamily based solely on sequence comparisons to known members. Therefore, we used a recently developed method HHsearch for sensitive detection of remote similarities between protein families represented as profile Hidden Markov Models enhanced by secondary structure. We carried out a comparison of known families of PD-(D/E)XK nucleases to the database comprising the COG and PFAM profiles corresponding to both functionally characterized as well as uncharacterized protein families to detect significant similarities. The initial candidates for new nucleases were subsequently verified by sequence-structure threading, comparative modeling, and identification of potential active site residues. In this article, we report identification of the PD-(D/E)XK nuclease domain in numerous proteins implicated in interactions with DNA but with unknown structure and mechanism of action (such as putative recombinase RmuC, DNA competence factor CoiA, a DNA-binding protein SfsA, a large human protein predicted to be a DNA repair enzyme, predicted archaeal transcription regulators, and the head completion protein of phage T4) and in proteins for which no function was assigned to date (such as YhcG, various phage proteins, novel candidates for restriction enzymes). Our results contributes to the reduction of "white spaces" on the sequence-structure-function map of the protein universe and will help to jump-start the experimental characterization of new nucleases, of which many may be of importance for the complete understanding of mechanisms that govern the evolution and stability of the genome.
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影响因子：
4.4
作者：
Feder M;Bujnicki JM
通讯作者：
Bujnicki JM
影响因子：
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作者：
Chmiel, AA;Bujnicki, JM;Skowronek, KJ
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Skowronek, KJ
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1.6
作者：
Bujnicki, JM;Rychlewski, L
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Rychlewski, L
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作者：
James, R;Penfold, CN;Kleanthous, C
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Kleanthous, C
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16
作者：
Hickman, AB;Li, Y;Dyda, F
通讯作者：
Dyda, F