6G3Z

Sulfolobus sulfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDPG

Summary for 6G3Z

• Entry DOI: 10.2210/pdb6g3z/pdb
• Related: 4UXD
• Descriptor: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase, 2-keto 3 deoxy 6 phospho gluconate, ISOPROPYL ALCOHOL, ... (4 entities in total)
• Functional Keywords: 2-keto-3-deoxygluconate aldolase, sulfolobus sulfataricus, 2-dehydro-3-deoxy-6-phospho-d-gluconate, lyase
• Biological source: Sulfolobus solfataricus
• Total number of polymer chains: 2
• Total formula weight: 67241.62

Authors

Crennell, S.J. (deposition date: 2018-03-26, release date: 2018-06-27, Last modification date: 2024-01-17)

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

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

Experimental method

X-RAY DIFFRACTION (2.35 Å)