A novel main-chain anion-binding site in proteins:: The nest.: A particular combination of φ,ψ values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions
A novel main-chain anion-binding site in proteins:: The nest.: A particular combination of φ,ψ values in successive residues gives rise to anion-binding sites that occur commonly and are found often at functionally important regions
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DOI：
10.1006/jmbi.2001.5227
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发表时间：
2002-01-11
影响因子：
5.6
通讯作者：
Milner-White, EJ
中科院分区：
文献类型：
--
作者：
Watson, JD;Milner-White, EJ
其中一个氨基酸残基可以被描述为γ（R）（或α（R））并且相邻的一个氨基酸残基可以被描述为γ（L）（或α（L））的主链构象主要导致三个主链NH基团（两个残基和随后的一个残基）形成可以容纳具有全部或部分负电荷的原子的凹陷。我们建议将此功能命名为nest。当存在时，带负电荷的原子也通过与NH基团的氢键而稳定。在平均蛋白质中，8%的残基参与了巢。通常占据巢的阴离子或部分带负电荷的原子可能是主链羰基氧原子，如回形针中的羰基氧原子，也称为Schellman环，以及丝氨酸蛋白酶的氧阴离子孔。它可以是磷酸基团，如在结合ATP和GTP的P环超家族中。经常观察到重叠的复合巢，如在P环中，其具有五个连续的NH基团，其结合核苷酸三磷酸的β磷酸基团。最长的化合物巢被发现围绕半胱氨酸结合的[2Fe 2S]和[4Fe 4S]铁硫中心，这也是阴离子;巢可能会鼓励更多的还原形式的结合。巢是一个新的功能，在这个意义上没有被描述为一个独特的主题与阴离子结合的潜力之前，虽然它发生的一些情况是熟悉的。(C)北京大学出版社.
Main-chain conformations where one amino acid residue can be described as gamma(R) (or alpha(R)) and an adjacent one as gamma(L) (or alpha(L)) mostly result in the three main-chain NH groups (of the two residues and the one following) forming a depression that can accommodate an atom with a whole or partial negative charge. We propose the name nest for this feature. The negatively charged atom, when present, is also stabilized by hydrogen-bonding with the NH groups. In an average protein, 8% of residues are involved in a nest. The anion, or partially negatively charged atom, that often occupies the nest may be a main-chain carbonyl oxygen atom as in the paperclip, also called the Schellman loop, and the oxyanion hole of serine proteases. It can be a phosphate group, as in the P-loop superfamily that binds ATP and GTP. Overlapping, compound, nests are observed often, as in the P-loop, which has five successive NH groups that bind the beta phosphate group of nucleotide triphosphate. The longest compound nests are found surrounding cysteine-bound [2Fe2S] and [4Fe4S] iron-sulfur centers, which are also anionic; nests may encourage binding of the more reduced forms. The nest is a novel feature in the sense of not having been described as a unique motif with anion-binding potential before, although some of the situations where it occurs are familiar. (C) 2002 Academic Press.