6XP3

Structure of human PYCR1 complexed with cyclopentanecarboxylic acid

Summary for 6XP3

• Entry DOI: 10.2210/pdb6xp3/pdb
• Descriptor: Pyrroline-5-carboxylate reductase 1, mitochondrial, SULFATE ION, cyclopentanecarboxylic acid, ... (4 entities in total)
• Functional Keywords: amino-acid biosynthesis, oxidoreductase, proline biosynthesis
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 5
• Total formula weight: 170828.32

Authors

Tanner, J.J.,Bogner, A.N. (deposition date: 2020-07-07, release date: 2020-11-04, Last modification date: 2023-10-18)

Primary citation

Christensen, E.M.,Bogner, A.N.,Vandekeere, A.,Tam, G.S.,Patel, S.M.,Becker, D.F.,Fendt, S.M.,Tanner, J.J.
In crystallo screening for proline analog inhibitors of the proline cycle enzyme PYCR1.
J.Biol.Chem., 295:18316-18327, 2020

PubMed Abstract: Pyrroline-5-carboxylate reductase 1 (PYCR1) catalyzes the biosynthetic half-reaction of the proline cycle by reducing Δ-pyrroline-5-carboxylate (P5C) to proline through the oxidation of NAD(P)H. Many cancers alter their proline metabolism by up-regulating the proline cycle and proline biosynthesis, and knockdowns of PYCR1 lead to decreased cell proliferation. Thus, evidence is growing for PYCR1 as a potential cancer therapy target. Inhibitors of cancer targets are useful as chemical probes for studying cancer mechanisms and starting compounds for drug discovery; however, there is a notable lack of validated inhibitors for PYCR1. To fill this gap, we performed a small-scale focused screen of proline analogs using X-ray crystallography. Five inhibitors of human PYCR1 were discovered: l-tetrahydro-2-furoic acid, cyclopentanecarboxylate, l-thiazolidine-4-carboxylate, l-thiazolidine-2-carboxylate, and -formyl l-proline (NFLP). The most potent inhibitor was NFLP, which had a competitive (with P5C) inhibition constant of 100 μm The structure of PYCR1 complexed with NFLP shows that inhibitor binding is accompanied by conformational changes in the active site, including the translation of an α-helix by 1 Å. These changes are unique to NFLP and enable additional hydrogen bonds with the enzyme. NFLP was also shown to phenocopy the knockdown in MCF10A H-RAS breast cancer cells by inhibiting proline biosynthesis and impairing spheroidal growth. In summary, we generated the first validated chemical probe of PYCR1 and demonstrated proof-of-concept for screening proline analogs to discover inhibitors of the proline cycle.

PubMed: 33109600
DOI: 10.1074/jbc.RA120.016106

Experimental method

X-RAY DIFFRACTION (1.93 Å)