Modular architecture of nucleotide-binding pockets

被引:25
作者
Gherardini, Pier Federico [1 ]
Ausiello, Gabriele [1 ]
Russell, Robert B. [2 ]
Helmer-Citterich, Manuela [1 ]
机构
[1] Univ Roma Tor Vergata, Ctr Mol Bioinformat, Dept Biol, I-00133 Rome, Italy
[2] Univ Heidelberg, D-69120 Heidelberg, Germany
关键词
CONVERGENT EVOLUTION; STRUCTURAL MOTIFS; ATP-BINDING; P-LOOP; PROTEINS; SEQUENCE; SITES; ADENINE; CLASSIFICATION; LIGANDS;
D O I
10.1093/nar/gkq090
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Recently, modularity has emerged as a general attribute of complex biological systems. This is probably because modular systems lend themselves readily to optimization via random mutation followed by natural selection. Although they are not traditionally considered to evolve by this process, biological ligands are also modular, being composed of recurring chemical fragments, and moreover they exhibit similarities reminiscent of mutations (e.g. the few atoms differentiating adenine and guanine). Many ligands are also promiscuous in the sense that they bind to many different protein folds. Here, we investigated whether ligand chemical modularity is reflected in an underlying modularity of binding sites across unrelated proteins. We chose nucleotides as paradigmatic ligands, because they can be described as composed of well-defined fragments (nucleobase, ribose and phosphates) and are quite abundant both in nature and in protein structure databases. We found that nucleotide-binding sites do indeed show a modular organization and are composed of fragment-specific protein structural motifs, which parallel the modular structure of their ligands. Through an analysis of the distribution of these motifs in different proteins and in different folds, we discuss the evolutionary implications of these findings and argue that the structural features we observed can arise both as a result of divergence from a common ancestor or convergent evolution.
引用
收藏
页码:3809 / 3816
页数:8
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