3PH4

Clostridium thermocellum Ribose-5-Phosphate Isomerase B with d-allose

3PH4 の概要

• エントリーDOI: 10.2210/pdb3ph4/pdb
• 関連するPDBエントリー: 3HE8 3HEE 3PH3
• 分子名称: Ribose-5-phosphate isomerase, D-ALLOSE (3 entities in total)
• 機能のキーワード: alpha-beta-alpha sandwich fold, isomerase
• 由来する生物種: Clostridium thermocellum
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 37006.00

構造登録者

Jung, J.,Kim, J.-K.,Yeom, S.-J.,Ahn, Y.-J.,Oh, D.-K.,Kang, L.-W. (登録日: 2010-11-03, 公開日: 2011-04-13, 最終更新日: 2023-11-01)

主引用文献

Jung, J.,Kim, J.K.,Yeom, S.J.,Ahn, Y.J.,Oh, D.K.,Kang, L.W.
Crystal structure of Clostridium thermocellum ribose-5-phosphate isomerase B reveals properties critical for fast enzyme kinetics.
Appl.Microbiol.Biotechnol., 90:517-527, 2011

PubMed Abstract: Ribose-5-phosphate isomerase (Rpi) catalyzes the conversion of D-ribose 5-phosphate (R5P) to D-ribulose 5-phosphate, which is an important step in the non-oxidative pathway of the pentose phosphate pathway and the Calvin cycle of photosynthesis. Recently, Rpis have been used to produce valuable rare sugars for industrial purposes. Of the Rpis, D-ribose-5-phosphate isomerase B from Clostridium thermocellum (CtRpi) has the fastest reactions kinetics. While Thermotoga maritime Rpi (TmRpi) has the same substrate specificity as CtRpi, the overall activity of CtRpi is approximately 200-fold higher than that of TmRpi. To understand the structural basis of these kinetic differences, we determined the crystal structures, at 2.1-Å resolution or higher, of CtRpi alone and bound to its substrates, R5P, D-ribose, and D-allose. Structural comparisons of CtRpi and TmRpi showed overall conservation of their structures with two notable differences. First, the volume of the CtRpi substrate binding pocket (SBP) was 20% less than that of the TmRpi SBP. Second, the residues next to the sugar-ring opening catalytic residue (His98) were different. We switched the key residues, involved in SBP shaping or catalysis, between CtRpi and TmRpi by site-directed mutagenesis, and studied the enzyme kinetics of the mutants. We found that tight interactions between the two monomers, narrow SBP width, and the residues near the catalytic residue are all critical for the fast enzyme kinetics of CtRpi.

PubMed: 21253719
DOI: 10.1007/s00253-011-3095-8

実験手法

X-RAY DIFFRACTION (2.07 Å)