4UXD

2-keto 3-deoxygluconate aldolase from Picrophilus torridus

4UXD の概要

• エントリーDOI: 10.2210/pdb4uxd/pdb
• 分子名称: 2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE, GLYCEROL, ISOPROPYL ALCOHOL, ... (7 entities in total)
• 機能のキーワード: tim barrel, lyase
• 由来する生物種: PICROPHILUS TORRIDUS
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 138880.10

構造登録者

Priftis, A.,Zaitsev, V.,Reher, M.,Johnsen, U.,Danson, M.J.,Taylor, G.L.,Schoenheit, P.,Crennell, S.J. (登録日: 2014-08-22, 公開日: 2015-09-30, 最終更新日: 2024-01-10)

主引用文献

Zaitsev, V.,Johnsen, U.,Reher, M.,Ortjohann, M.,Taylor, G.L.,Danson, M.J.,Schonheit, P.,Crennell, S.J.
Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate.
Biochemistry, 57:3797-3806, 2018

PubMed Abstract: The thermoacidophilic archaea Picrophilus torridus and Sulfolobus solfataricus catabolize glucose via a nonphosphorylative Entner-Doudoroff pathway and a branched Entner-Doudoroff pathway, respectively. Key enzymes for these Entner-Doudoroff pathways are the aldolases, 2-keto-3-deoxygluconate aldolase (KDG-aldolase) and 2-keto-3-deoxy-6-phosphogluconate aldolase [KD(P)G-aldolase]. KDG-aldolase from P. torridus (Pt-KDG-aldolase) is highly specific for the nonphosphorylated substrate, 2-keto-3-deoxygluconate (KDG), whereas KD(P)G-aldolase from S. solfataricus [Ss-KD(P)G-aldolase] is an enzyme that catalyzes the cleavage of both KDG and 2-keto-3-deoxy-6-phosphogluconate (KDPG), with a preference for KDPG. The structural basis for the high specificity of Pt-KDG-aldolase for KDG as compared to the more promiscuous Ss-KD(P)G-aldolase has not been analyzed before. In this work, we report the elucidation of the structure of Ss-KD(P)G-aldolase in complex with KDPG at 2.35 Å and that of KDG-aldolase from P. torridus at 2.50 Å resolution. By superimposition of the active sites of the two enzymes, and subsequent site-directed mutagenesis studies, a network of four amino acids, namely, Arg106, Tyr132, Arg237, and Ser241, was identified in Ss-KD(P)G-aldolase that interact with the negatively charged phosphate group of KDPG, thereby increasing the affinity of the enzyme for KDPG. This KDPG-binding network is absent in Pt-KDG-aldolase, which explains the low catalytic efficiency of KDPG cleavage.

PubMed: 29812914
DOI: 10.1021/acs.biochem.8b00535

実験手法

X-RAY DIFFRACTION (2.5 Å)