8ELM image
Entry Detail
PDB ID:
8ELM
Keywords:
Title:
Apo human biliverdin reductase beta (293K)
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-09-26
Release Date:
2023-09-06
Method Details:
Experimental Method:
Resolution:
2.19 Å
R-Value Free:
0.22
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Flavin reductase (NADPH)
Chain IDs:A
Chain Length:206
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle.
Front Mol Biosci 10 1244587 1244587 (2023)
PMID: 37645217 DOI: 10.3389/fmolb.2023.1244587

Abstact

Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that "clamps" the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme.

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