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4UXD

2-keto 3-deoxygluconate aldolase from Picrophilus torridus

Summary for 4UXD
Entry DOI10.2210/pdb4uxd/pdb
Descriptor2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE, GLYCEROL, ISOPROPYL ALCOHOL, ... (7 entities in total)
Functional Keywordstim barrel, lyase
Biological sourcePICROPHILUS TORRIDUS
Total number of polymer chains4
Total formula weight138880.10
Authors
Priftis, A.,Zaitsev, V.,Reher, M.,Johnsen, U.,Danson, M.J.,Taylor, G.L.,Schoenheit, P.,Crennell, S.J. (deposition date: 2014-08-22, release date: 2015-09-30, Last modification date: 2024-01-10)
Primary citationZaitsev, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.5 Å)
Structure validation

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数据于2025-07-02公开中

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