8SWQ

Structure of K. lactis PNP bound to transition state analog DADMe-IMMUCILLIN H and sulfate

Summary for 8SWQ

• Entry DOI: 10.2210/pdb8swq/pdb
• Related: 8SWP 8SWR 8SWS 8SWT 8SWU
• Descriptor: Purine nucleoside phosphorylase, 7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one, SULFATE ION, ... (5 entities in total)
• Functional Keywords: pentosyltransferase, purine nucleoside phosphorylase, transferase
• Biological source: Kluyveromyces lactis NRRL Y-1140
• Total number of polymer chains: 6
• Total formula weight: 204383.61

Authors

Fedorov, E.,Ghosh, A. (deposition date: 2023-05-19, release date: 2023-10-18, Last modification date: 2024-11-06)

Primary citation

Minnow, Y.V.T.,Schramm, V.L.,Almo, S.C.,Ghosh, A.
Phosphate Binding in PNP Alters Transition-State Analogue Affinity and Subunit Cooperativity.
Biochemistry, 62:3116-3125, 2023

PubMed Abstract: Purine nucleoside phosphorylases (PNPs) catalyze the phosphorolysis of 6-oxypurine nucleosides with an HPO dianion nucleophile. Nucleosides and phosphate occupy distinct pockets in the PNP active site. Evaluation of the HPO site by mutagenesis, cooperative binding studies, and thermodynamic and structural analysis demonstrate that alterations in the HPO binding site can render PNP inactive and significantly impact subunit cooperativity and binding to transition-state analogue inhibitors. Cooperative interactions between the cationic transition-state analogue and the anionic HPO nucleophile demonstrate the importance of reforming the transition-state ensemble for optimal inhibition with transition-state analogues. Altered phosphate binding in the catalytic site mutants helps to explain one of the known lethal PNP deficiency syndromes in humans.

PubMed: 37812583
DOI: 10.1021/acs.biochem.3c00264

Experimental method

X-RAY DIFFRACTION (1.979 Å)