2i56
From Proteopedia
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Crystal structure of L-Rhamnose Isomerase from Pseudomonas stutzeri with L-Rhamnose
Overview
Pseudomonas stutzeri L-rhamnose isomerase (P. stutzeri L-RhI) can, efficiently catalyze the isomerization between various aldoses and, ketoses, showing a broad substrate specificity compared to L-RhI from, Escherichia coli (E. coli L-RhI). To understand the relationship between, structure and substrate specificity, the crystal structures of P. stutzeri, L-RhI alone and in complexes with L-rhamnose and D-allose which has, different configurations of C4 and C5 from L-rhamnose, were determined at, a resolution of 2.0 A, 1.97 A, and 1.97 A, respectively. P. stutzeri L-RhI, has a large domain with a (beta/alpha)(8) barrel fold and an additional, small domain composed of seven alpha-helices, forming a homo tetramer, as, found in E. coli L-RhI and D-xylose isomerases (D-XIs) from various, microorganisms. The beta1-alpha1 loop (Gly60-Arg76) of P. stutzeri L-RhI, is involved in the substrate binding of a neighbouring molecule, as found, in D-XIs, while in E. coli L-RhI, the corresponding beta1-alpha1 loop is, extended (Asp52-Arg78) and covers the substrate-binding site of the same, molecule. The complex structures of P. stutzeri L-RhI with L-rhamnose and, D-allose show that both substrates are nicely fitted to the, substrate-binding site. The part of the substrate-binding site interacting, with the substrate at the 1, 2, and 3 positions is equivalent to E. coli, L-RhI, and the other part interacting with the 4, 5, and 6 positions is, similar to D-XI. In E. coli L-RhI, the beta1-alpha1 loop creates an unique, hydrophobic pocket at the the 4, 5, and 6 positions, leading to the, strictly recognition of L-rhamnose as the most suitable substrate, while, in P. stutzeri L-RhI, there is no corresponding hydrophobic pocket where, Phe66 from a neighbouring molecule merely forms hydrophobic interactions, with the substrate, leading to the loose substrate recognition at the 4, 5, and 6 positions.
About this Structure
2I56 is a Single protein structure of sequence from Pseudomonas stutzeri with and as ligands. Active as L-rhamnose isomerase, with EC number 5.3.1.14 Full crystallographic information is available from OCA.
Reference
The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity., Yoshida H, Yamada M, Ohyama Y, Takada G, Izumori K, Kamitori S, J Mol Biol. 2007 Feb 2;365(5):1505-16. Epub 2006 Nov 6. PMID:17141803
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