5JAB

Structure of the biliverdin reductase Rv2074 from Mycobacterium tuberculosis in complex with F420


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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This is version 1.2 of the entry. See complete history


Literature

Rv2074 is a novel F420 H2 -dependent biliverdin reductase in Mycobacterium tuberculosis.

Ahmed, F.H.Mohamed, A.E.Carr, P.D.Lee, B.M.Condic-Jurkic, K.O'Mara, M.L.Jackson, C.J.

(2016) Protein Sci 25: 1692-1709

  • DOI: https://doi.org/10.1002/pro.2975
  • Primary Citation of Related Structures:  
    5JAB

  • PubMed Abstract: 
  • Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction ...

    Bilirubin is a potent antioxidant that is produced from the reduction of the heme degradation product biliverdin. In mammalian cells and Cyanobacteria, NADH/NADPH-dependent biliverdin reductases (BVRs) of the Rossmann-fold have been shown to catalyze this reaction. Here, we describe the characterization of Rv2074 from Mycobacterium tuberculosis, which belongs to a structurally and mechanistically distinct family of F420 H2 -dependent BVRs (F-BVRs) that are exclusively found in Actinobacteria. We have solved the crystal structure of Rv2074 bound to its cofactor, F420 , and used this alongside molecular dynamics simulations, site-directed mutagenesis and NMR spectroscopy to elucidate its catalytic mechanism. The production of bilirubin by Rv2074 could exploit the anti-oxidative properties of bilirubin and contribute to the range of immuno-evasive mechanisms that have evolved in M. tuberculosis to allow persistent infection.


    Organizational Affiliation

    Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Biliverdin reductase Rv2074A, B, C, D135Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv2074MTCY49.13
EC: 1.3.98
UniProt
Find proteins for P9WLL7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WLL7 
Go to UniProtKB:  P9WLL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WLL7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.756α = 90
b = 88.62β = 90
c = 98.625γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-31
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations