4UXD
2-keto 3-deoxygluconate aldolase from Picrophilus torridus
Summary for 4UXD
Entry DOI | 10.2210/pdb4uxd/pdb |
Descriptor | 2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE, GLYCEROL, ISOPROPYL ALCOHOL, ... (7 entities in total) |
Functional Keywords | tim barrel, lyase |
Biological source | PICROPHILUS TORRIDUS |
Total number of polymer chains | 4 |
Total formula weight | 138880.10 |
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 citation | 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 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: 29812914DOI: 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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