Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.
Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.
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DOI：
10.1186/gb-2002-3-4-research0016
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发表时间：
2002
期刊：
影响因子：
12.3
通讯作者：
Hardtke CS
中科院分区：
文献类型：
--
作者：
Kosarev P;Mayer KF;Hardtke CS
在计算分析中，环指结构域是拟南芥蛋白质组中最常检测到的结构域之一。事实上，它在拟南芥中比在其他真核生物基因组中更丰富。然而，计算分析可能会错误地将密切相关的PHD和LIM基序的模糊域分类为RING域。因此，我们开始定义一组有序的拟南芥RING结构域的基础上，最近的结构数据进行评估预测的结构域。用当前InterPro版本检查蛋白质组预测446个RING结构域。我们评估了每个检测到的域，结果消除了59个假阳性。其余的387个域进行了分组的聚类分析，并根据其金属配体的安排。我们进一步定义了新的模式，用于蛋白质组的额外计算分析。它们是基于最近的结构数据，使相关的RING，PHD和LIM结构域之间的歧视。这些模式使我们能够以不同程度的确定性来预测某个特定的结构域是否真的有可能形成一个环指。总之，387结构域具有形成RING型交叉支撑结构的显著潜力。这些RING域中的许多与预测的PHD域重叠;然而，RING域签名大多占优势。因此，拟南芥中PHD结构域的丰度被显著高估。RING结构域的聚类分析定义了蛋白质组，这些蛋白质组经常在RING结构域之外显示出显著的相似性。这些群体记录了其成员的共同进化起源，并可能代表具有重叠功能的基因。
In computational analysis, the RING-finger domain is one of the most frequently detected domains in the Arabidopsis proteome. In fact, it is more abundant in Arabidopsis than in other eukaryotic genomes. However, computational analysis might classify ambiguous domains of the closely related PHD and LIM motifs as RING domains by mistake. Thus, we set out to define an ordered set of Arabidopsis RING domains by evaluating predicted domains on the basis of recent structural data. Inspection of the proteome with a current InterPro release predicts 446 RING domains. We evaluated each detected domain and as a result eliminated 59 false positives. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement. We further defined novel patterns for additional computational analyses of the proteome. They were based on recent structural data that enable discrimination between the related RING, PHD and LIM domains. These patterns allow us to predict with different degrees of certainty whether a particular domain is indeed likely to form a RING finger. In summary, 387 domains have a significant potential to form a RING-type cross-brace structure. Many of these RING domains overlap with predicted PHD domains; however, the RING domain signature mostly prevails. Thus, the abundance of PHD domains in Arabidopsis has been significantly overestimated. Cluster analysis of the RING domains defines groups of proteins, which frequently show significant similarity outside the RING domain. These groups document a common evolutionary origin of their members and potentially represent genes of overlapping functionality.
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