1GCU

CRYSTAL STRUCTURE OF RAT BILIVERDIN REDUCTASE AT 1.4 A

• PDB DOI: https://doi.org/10.2210/pdb1GCU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-08-08 Released: 2001-02-08 
• Deposition Author(s): Kikuchi, A., Park, S.Y., Shiro, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Literature

Crystal structure of rat biliverdin reductase.

Kikuchi, A., Park, S.Y., Miyatake, H., Sun, D., Sato, M., Yoshida, T., Shiro, Y.

(2001) Nat Struct Biol 8: 221-225

• PubMed: 11224565 
• DOI: https://doi.org/10.1038/84955
• Primary Citation of Related Structures:  
  1GCU


• PubMed Abstract: 
  

  Biliverdin reductase (BVR) is a soluble cytoplasmic enzyme that catalyzes the conversion of biliverdin to bilirubin using NADH or NADPH as electron donor. Bilirubin is a significant biological antioxidant, but it is also neurotoxic and the cause of kernicterus. In this study, we have determined the crystal structure of rat BVR at 1.4 A resolution. The structure contains two domains: an N-terminal domain characteristic of a dinucleotide binding fold (Rossmann fold) and a C-terminal domain that is predominantly an antiparallel six-stranded beta-sheet. Based on this structure, we propose modes of binding for NAD(P)H and biliverdin, and a possible mechanism for the enzyme.

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Organizational Affiliation: 

RIKEN Harima Institute/SPring-8, Sayo, Hyogo 679-5148, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.61 kDa 
• Atom Count: 2,629 
• Modelled Residue Count: 292 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BILIVERDIN REDUCTASE A	A	295	Rattus norvegicus	Mutation(s): 0  EC: 1.3.1.24
UniProt
Find proteins for P46844 (Rattus norvegicus) Explore P46844  Go to UniProtKB:  P46844

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.682	α = 90
b = 70.487	β = 90
c = 87.866	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-08 
Deposition Author(s): Kikuchi, A., Park, S.Y., Shiro, Y.

Revision History  

• Version 1.0: 2001-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references