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Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.
Structure. 1994 Jul 15; 2(7):651-68.S

Abstract

BACKGROUND

The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction product, ribulose 5-phosphate, to ribose 5-phosphate. Crystallographic study of complexes with coenzyme and substrate explain the NADP dependence which determines the enzyme's metabolic role and support the proposed general base-general acid mechanism.

RESULTS

The refined structures of binary coenzyme/analogue complexes show that Arg33 is ordered by binding the 2'-phosphate, and provides one face of the adenine site. The nicotinamide, while less tightly bound, is more extended when reduced than when oxidized. All substrate binding residues are conserved; the 3-hydroxyl of 6-phosphogluconate is hydrogen bonded to N zeta of Lys183 and the 3-hydrogen points towards the oxidized nicotinamide. The 6-phosphate replaces a tightly bound sulphate in the apo-enzyme.

CONCLUSIONS

NADP specificity is achieved primarily by Arg33 which binds the 2'-phosphate but, in its absence, obscures the adenine pocket. The bound oxidized nicotinamide is syn; hydride transfer from bound substrate to the nicotinamide si- face is achieved with a small movement of the nicotinamide nucleotide. Lys183 may act as general base. A water bound to Gly130 in the coenzyme domain is the most likely acid required in decarboxylation. The dihydronicotinamide ring of NADPH competes for ligands with the 1-carboxyl of 6-phosphogluconate.

Authors+Show Affiliations

University of Oxford, Laboratory of Molecular Biophysics, UK.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

7922042

Citation

Adams, M J., et al. "Crystallographic Study of Coenzyme, Coenzyme Analogue and Substrate Binding in 6-phosphogluconate Dehydrogenase: Implications for NADP Specificity and the Enzyme Mechanism." Structure (London, England : 1993), vol. 2, no. 7, 1994, pp. 651-68.
Adams MJ, Ellis GH, Gover S, et al. Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism. Structure. 1994;2(7):651-68.
Adams, M. J., Ellis, G. H., Gover, S., Naylor, C. E., & Phillips, C. (1994). Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism. Structure (London, England : 1993), 2(7), 651-68.
Adams MJ, et al. Crystallographic Study of Coenzyme, Coenzyme Analogue and Substrate Binding in 6-phosphogluconate Dehydrogenase: Implications for NADP Specificity and the Enzyme Mechanism. Structure. 1994 Jul 15;2(7):651-68. PubMed PMID: 7922042.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism. AU - Adams,M J, AU - Ellis,G H, AU - Gover,S, AU - Naylor,C E, AU - Phillips,C, PY - 1994/7/15/pubmed PY - 1994/7/15/medline PY - 1994/7/15/entrez SP - 651 EP - 68 JF - Structure (London, England : 1993) JO - Structure VL - 2 IS - 7 N2 - BACKGROUND: The nicotinamide adenine dinucleotide phosphate (NADP)-dependent oxidative decarboxylase, 6-phosphogluconate dehydrogenase, is a major source of reduced coenzyme for synthesis. Enzymes later in the pentose phosphate pathway convert the reaction product, ribulose 5-phosphate, to ribose 5-phosphate. Crystallographic study of complexes with coenzyme and substrate explain the NADP dependence which determines the enzyme's metabolic role and support the proposed general base-general acid mechanism. RESULTS: The refined structures of binary coenzyme/analogue complexes show that Arg33 is ordered by binding the 2'-phosphate, and provides one face of the adenine site. The nicotinamide, while less tightly bound, is more extended when reduced than when oxidized. All substrate binding residues are conserved; the 3-hydroxyl of 6-phosphogluconate is hydrogen bonded to N zeta of Lys183 and the 3-hydrogen points towards the oxidized nicotinamide. The 6-phosphate replaces a tightly bound sulphate in the apo-enzyme. CONCLUSIONS: NADP specificity is achieved primarily by Arg33 which binds the 2'-phosphate but, in its absence, obscures the adenine pocket. The bound oxidized nicotinamide is syn; hydride transfer from bound substrate to the nicotinamide si- face is achieved with a small movement of the nicotinamide nucleotide. Lys183 may act as general base. A water bound to Gly130 in the coenzyme domain is the most likely acid required in decarboxylation. The dihydronicotinamide ring of NADPH competes for ligands with the 1-carboxyl of 6-phosphogluconate. SN - 0969-2126 UR - https://www.unboundmedicine.com/medline/citation/7922042/Crystallographic_study_of_coenzyme_coenzyme_analogue_and_substrate_binding_in_6_phosphogluconate_dehydrogenase:_implications_for_NADP_specificity_and_the_enzyme_mechanism_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0969-2126(00)00066-6 DB - PRIME DP - Unbound Medicine ER -