5OOH

Human biliverdin IX beta reductase: NADP/Erythrosin extra bluish ternary complex

Summary for 5OOH

• Entry DOI: 10.2210/pdb5ooh/pdb
• Descriptor: Flavin reductase (NADPH), NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, GLYCEROL, ... (5 entities in total)
• Functional Keywords: biliverdin reductase, oxidoreductase
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm : P30043
• Total number of polymer chains: 1
• Total formula weight: 23819.74

Authors

Manso, J.A.,Pereira, P.J.B. (deposition date: 2017-08-07, release date: 2018-03-07, Last modification date: 2024-01-17)

Primary citation

Nesbitt, N.M.,Zheng, X.,Li, Z.,Manso, J.A.,Yen, W.Y.,Malone, L.E.,Ripoll-Rozada, J.,Pereira, P.J.B.,Mantle, T.J.,Wang, J.,Bahou, W.F.
In silicoand crystallographic studies identify key structural features of biliverdin IX beta reductase inhibitors having nanomolar potency.
J. Biol. Chem., 293:5431-5446, 2018

PubMed Abstract: Heme cytotoxicity is minimized by a two-step catabolic reaction that generates biliverdin (BV) and bilirubin (BR) tetrapyrroles. The second step is regulated by two non-redundant biliverdin reductases (IXα (BLVRA) and IXβ (BLVRB)), which retain isomeric specificity and NAD(P)H-dependent redox coupling linked to BR's antioxidant function. Defective BLVRB enzymatic activity with antioxidant mishandling has been implicated in metabolic consequences of hematopoietic lineage fate and enhanced platelet counts in humans. We now outline an integrated platform of and crystallographic studies for the identification of an initial class of compounds inhibiting BLVRB with potencies in the nanomolar range. We found that the most potent BLVRB inhibitors contain a tricyclic hydrocarbon core structure similar to the isoalloxazine ring of flavin mononucleotide and that both xanthene- and acridine-based compounds inhibit BLVRB's flavin and dichlorophenolindophenol (DCPIP) reductase functions. Crystallographic studies of ternary complexes with BLVRB-NADP-xanthene-based compounds confirmed inhibitor binding adjacent to the cofactor nicotinamide and interactions with the Ser-111 side chain. This residue previously has been identified as critical for maintaining the enzymatic active site and cellular reductase functions in hematopoietic cells. Both acridine- and xanthene-based compounds caused selective and concentration-dependent loss of redox coupling in BLVRB-overexpressing promyelocytic HL-60 cells. These results provide promising chemical scaffolds for the development of enhanced BLVRB inhibitors and identify chemical probes to better dissect the role of biliverdins, alternative substrates, and BLVRB function in physiologically relevant cellular contexts.

PubMed: 29487133
DOI: 10.1074/jbc.RA118.001803

Experimental method

X-RAY DIFFRACTION (1.2 Å)