Local structural alignment and classification of TIM barrel domains

Abstract

TIM barrel domain is widely studied since it is one of most common structure and mediates diverse function maintaining overall structure. TIM barrel domain’s function is determined by local structural environment at the C-terminal end of barrel structure. We classified TIM barrel domains by local structural alignment tool, LSHEBA, to understand characteristics of TIM barrel domain’s functionalvariation. TIM barrel domains classified as the same cluster share common structure, function and ligands. Over 80% of TIM barrels in clusters share exactly the same catalytic function. Comparing clustering result with that of SCOP, we found that it’s important to know local structural environment of TIM barrel domains rather than overallstructure to understand specific structural detail of TIM barrel function. Non TIM barrel domains were associated to make different domain combination to form a different function. The relationship between domain combination, we suggested expected evolutional history. We finally analyzed the characteristics of amino acids around ligand interface. Corresponding Author: Changwon Keum (Email: keum4988@empal.com) Introduction TIM barrel fold, composed of 8 continuous (β/α) motifs, has been widely studied since it is one of most common folds as nearly 10% of enzyme known so far have TIM barrel domain(Nozomi Nagano 2001). However, their sequence similarity is not high enough to detect their evolutional relationship and structural similarity. TIM barrel fold is also one of most functionally versatile folds(Wierenga 2001). The active sites of TIM barrel always come at the end of C-terminal barrel composed of inside β-sheets. This suggests TIM barrel have evolved from ancestral TIM barrel with divergent evolution(Rayment 2004). The functional diversity of TIM barrel comes from the fact that the TIM barrel function can be changed by slight variation around the active site, loops connecting C-terminal inside β-sheets and outside α-helices. Function variation of TIM barrel is dividedinto two categories, substrate specificity and catalytic activity. Variation at inside barrel changes substrate specificity of the TIM barrels. On the other hand, variation around active site changes catalytic activity (Altamirano 2000). These TIM barrel‘s two ways of function creation made it an efficient fold to manipulate new enzyme activity. One fold-many function character of TIM barrel makesit difficult to assign function based on structure(Nozomi Nagano 2002).Just recognizing overall structure of TIM barrel is not enough to understand relationship between structure and function of TIM barrel domains. Many protein structural databases such as SCOP (Alexey G. Murzin 1995) and CATH (CA Orengo and Thornton 1997) classified TIM barrels according to their structures. However, TIM barrel classification by these databases does not detect specific difference among TIM barrel domains with different functions since TIM barrel domains in each family from the database have diverse function, not unique function. Here we tried to understand the relationship between structure and function of TIM barrel domain by local structural alignment of TIM barrel domains using LSHEBA (Lee 2000), a local structure alignment tool. We classified the TIM barrel structures using the result of structural alignment between TIM barrel domains. We tried to find structural and functional characteristics of each cluster and the relationship between ligand and function of TIM barrel domains. We also found the evolutional history between each clusters by considering domain combination.