5ooh

From Proteopedia

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

PDB ID 5ooh

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Structural highlights

5ooh is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.2Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BLVRB_HUMAN Broad specificity oxidoreductase that catalyzes the NADPH-dependent reduction of a variety of flavins, such as riboflavin, FAD or FMN, biliverdins, methemoglobin and PQQ (pyrroloquinoline quinone). Contributes to heme catabolism and metabolizes linear tetrapyrroles. Can also reduce the complexed Fe(3+) iron to Fe(2+) in the presence of FMN and NADPH. In the liver, converts biliverdin to bilirubin.^[1]

Publication Abstract from PubMed

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 (IXalpha[BLVRA] and IXbeta [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 in silico 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.

In silico and crystallographic studies identify key structural features of biliverdin IXbeta reductase inhibitors having nanomolar potency.,Nesbitt NM, Zheng X, Li Z, Manso JA, Yen WY, Malone LE, Ripoll-Rozada J, Pereira PJB, Mantle TJ, Wang J, Bahou WF J Biol Chem. 2018 Feb 27. pii: RA118.001803. doi: 10.1074/jbc.RA118.001803. PMID:29487133^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Cunningham O, Gore MG, Mantle TJ. Initial-rate kinetics of the flavin reductase reaction catalysed by human biliverdin-IXbeta reductase (BVR-B). Biochem J. 2000 Jan 15;345 Pt 2:393-9. PMID:10620517
↑ Nesbitt NM, Zheng X, Li Z, Manso JA, Yen WY, Malone LE, Ripoll-Rozada J, Pereira PJB, Mantle TJ, Wang J, Bahou WF. In silico and crystallographic studies identify key structural features of biliverdin IXbeta reductase inhibitors having nanomolar potency. J Biol Chem. 2018 Feb 27. pii: RA118.001803. doi: 10.1074/jbc.RA118.001803. PMID:29487133 doi:http://dx.doi.org/10.1074/jbc.RA118.001803