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Catalytic reaction mechanism of Pseudomonas stutzeri L-rhamnose isomerase deduced from X-ray structures.

Yoshida H, Yamaji M, Ishii T, Izumori K, Kamitori S
FEBS J 277 1045-57 (2010)
Related entries: 2hcv, 2i56, 2i57, 3itl, 3ito, 3itv, 3itx, 3ity, 3iud, 3iuh, 3iui

Cited: 16 times
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Abstract

L-Rhamnose isomerase (L-RhI) catalyzes the reversible isomerization of L-rhamnose to L-rhamnulose. Pseudomonas stutzeril-RhI, with a broad substrate specificity, can catalyze not only the isomerization of L-rhamnose, but also that between D-allose and D-psicose. For the aldose-ketose isomerization by L-RhI, a metal-mediated hydride-shift mechanism has been proposed, but the catalytic mechanism is still not entirely understood. To elucidate the entire reaction mechanism, the X-ray structures of P. stutzeril-RhI in an Mn(2+)-bound form, and of two inactive mutant forms of P. stutzeril-RhI (S329K and D327N) in a complex with substrate/product, were determined. The structure of the Mn(2+)-bound enzyme indicated that the catalytic site interconverts between two forms with the displacement of the metal ion to recognize both pyranose and furanose ring substrates. Solving the structures of S329K-substrates allowed us to examine the metal-mediated hydride-shift mechanism of L-RhI in detail. The structural analysis of D327N-substrates and additional modeling revealed Asp327 to be responsible for the ring opening of furanose, and a water molecule coordinating with the metal ion to be involved in the ring opening of pyranose.

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  1. Enzymatic approaches to rare sugar production. Zhang W, Zhang T, Jiang B, Mu W. Biotechnol Adv 35 267-274 (2017)
  2. L-Rhamnose isomerase and its use for biotechnological production of rare sugars. Xu W, Zhang W, Zhang T, Jiang B, Mu W. Appl Microbiol Biotechnol 100 2985-2992 (2016)

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  1. Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme. Ben-David M, Wieczorek G, Elias M, Silman I, Sussman JL, Tawfik DS. J Mol Biol 425 1028-1038 (2013)
  2. Characterization of a thermophilic L-rhamnose isomerase from Caldicellulosiruptor saccharolyticus ATCC 43494. Lin CJ, Tseng WC, Fang TY. J Agric Food Chem 59 8702-8708 (2011)
  3. Rhamnose-inducible gene expression in Listeria monocytogenes. Fieseler L, Schmitter S, Teiserskas J, Loessner MJ. PLoS One 7 e43444 (2012)
  4. Structure-based studies on the metal binding of two-metal-dependent sugar isomerases. Prabhu P, Doan TN, Tiwari M, Singh R, Kim SC, Hong MK, Kang YC, Kang LW, Lee JK. FEBS J 281 3446-3459 (2014)
  5. X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates. Yoshida H, Yoshihara A, Ishii T, Izumori K, Kamitori S. Appl Microbiol Biotechnol 100 10403-10415 (2016)
  6. Crystal structures of rare disaccharides, α-D-glucopyranosyl β-D-psicofuranoside, and α-D-galactopyranosyl β-D-psicofuranoside. Kamitori S, Ueda A, Tahara Y, Yoshida H, Ishii T, Uenishi J. Carbohydr Res 346 1182-1185 (2011)
  7. Dibutylsilylene-pentose bis-chelates: on the glycoses' binding sites for strongly Lewis-acidic centres. Schulten J, Klüfers P. Carbohydr Res 346 1767-1775 (2011)
  8. Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of Pseudomonas stutzeri L-rhamnose isomerase. Yoshida H, Takeda K, Izumori K, Kamitori S. Protein Eng Des Sel 23 919-927 (2010)
  9. Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. Yoshida H, Yoshihara A, Teraoka M, Yamashita S, Izumori K, Kamitori S. FEBS Open Bio 3 35-40 (2013)


Related citations provided by authors (1)

  1. 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 365 1505-16 (2007)

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