8JQ4

Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with L-rhamnose

Summary for 8JQ4

• Entry DOI: 10.2210/pdb8jq4/pdb
• Related: 8JQ3
• Descriptor: L-rhamnose isomerase, MANGANESE (II) ION, beta-L-rhamnopyranose, ... (5 entities in total)
• Functional Keywords: tim barrel, isomerase
• Biological source: Lacticaseibacillus rhamnosus
• Total number of polymer chains: 4
• Total formula weight: 200576.38

Authors

Yoshida, H.,Yoshihara, A. (deposition date: 2023-06-13, release date: 2024-03-13)

Primary citation

Yoshida, H.,Yamamoto, N.,Kurahara, L.H.,Izumori, K.,Yoshihara, A.
X-ray structure and characterization of a probiotic Lactobacillus rhamnosus Probio-M9 L-rhamnose isomerase.
Appl.Microbiol.Biotechnol., 108:249-249, 2024

PubMed Abstract: A recombinant L-rhamnose isomerase (L-RhI) from probiotic Lactobacillus rhamnosus Probio-M9 (L. rhamnosus Probio-M9) was expressed. L. rhamnosus Probio-M9 was isolated from human colostrum and identified as a probiotic lactic acid bacterium, which can grow using L-rhamnose. L-RhI is one of the enzymes involved in L-rhamnose metabolism and catalyzes the reversible isomerization between L-rhamnose and L-rhamnulose. Some L-RhIs were reported to catalyze isomerization not only between L-rhamnose and L-rhamnulose but also between D-allulose and D-allose, which are known as rare sugars. Those L-RhIs are attractive enzymes for rare sugar production and have the potential to be further improved by enzyme engineering; however, the known crystal structures of L-RhIs recognizing rare sugars are limited. In addition, the optimum pH levels of most reported L-RhIs are basic rather than neutral, and such a basic condition causes non-enzymatic aldose-ketose isomerization, resulting in unexpected by-products. Herein, we report the crystal structures of L. rhamnosus Probio-M9 L-RhI (LrL-RhI) in complexes with L-rhamnose, D-allulose, and D-allose, which show enzyme activity toward L-rhamnose, D-allulose, and D-allose in acidic conditions, though the activity toward D-allose was low. In the complex with L-rhamnose, L-rhamnopyranose was found in the catalytic site, showing favorable recognition for catalysis. In the complex with D-allulose, D-allulofuranose and ring-opened D-allulose were observed in the catalytic site. However, bound D-allose in the pyranose form was found in the catalytic site of the complex with D-allose, which was unfavorable for recognition, like an inhibition mode. The structure of the complex may explain the low activity toward D-allose. KEY POINTS: • Crystal structures of LrL-RhI in complexes with substrates were determined. • LrL-RhI exhibits enzyme activity toward L-rhamnose, D-allulose, and D-allose. • The LrL-RhI is active in acidic conditions.

PubMed: 38430263
DOI: 10.1007/s00253-024-13075-9

Experimental method

X-RAY DIFFRACTION (1.61 Å)