The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity.
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.
Yoshida
Hiromi
H
Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.
Yamada
Mitsugu
M
Ohyama
Yuya
Y
Takada
Goro
G
Izumori
Ken
K
Kamitori
Shigehiro
S
D019747:Aldose-Ketose Isomerases / Q000737:chemistry*; D000818:Animals; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D005947:Glucose / Q000737:chemistry*; D006376:Helminths / Q000201:enzymology; D008670:Metals / Q000378:metabolism; D008958:Models, Molecular; D009005:Monosaccharides / Q000737:chemistry; D017433:Protein Structure, Secondary; D021122:Protein Subunits / Q000737:chemistry; D044223:Pseudomonas stutzeri / Q000201:enzymology*; D012210:Rhamnose / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
D008670:Metals; D009005:Monosaccharides; D021122:Protein Subunits; C002055:allose; D019747:Aldose-Ketose Isomerases; C062878:L-rhamnose isomerase; C023298:xylose isomerase; D005947:Glucose; D012210:Rhamnose