4L2N

Understanding Extradiol Dioxygenase Mechanism in NAD+ Biosynthesis by Viewing Catalytic Intermediates - ligand-free structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

An Iron Reservoir to the Catalytic Metal: THE RUBREDOXIN IRON IN AN EXTRADIOL DIOXYGENASE.

Liu, F.Geng, J.Gumpper, R.H.Barman, A.Davis, I.Ozarowski, A.Hamelberg, D.Liu, A.

(2015) J Biol Chem 290: 15621-15634

  • DOI: https://doi.org/10.1074/jbc.M115.650259
  • Primary Citation of Related Structures:  
    4HSJ, 4HVO, 4HVQ, 4L2N

  • PubMed Abstract: 

    The rubredoxin motif is present in over 74,000 protein sequences and 2,000 structures, but few have known functions. A secondary, non-catalytic, rubredoxin-like iron site is conserved in 3-hydroxyanthranilate 3,4-dioxygenase (HAO), from single cellular sources but not multicellular sources. Through the population of the two metal binding sites with various metals in bacterial HAO, the structural and functional relationship of the rubredoxin-like site was investigated using kinetic, spectroscopic, crystallographic, and computational approaches. It is shown that the first metal presented preferentially binds to the catalytic site rather than the rubredoxin-like site, which selectively binds iron when the catalytic site is occupied. Furthermore, an iron ion bound to the rubredoxin-like site is readily delivered to an empty catalytic site of metal-free HAO via an intermolecular transfer mechanism. Through the use of metal analysis and catalytic activity measurements, we show that a downstream metabolic intermediate can selectively remove the catalytic iron. As the prokaryotic HAO is often crucial for cell survival, there is a need for ensuring its activity. These results suggest that the rubredoxin-like site is a possible auxiliary iron source to the catalytic center when it is lost during catalysis in a pathway with metabolic intermediates of metal-chelating properties. A spare tire concept is proposed based on this biochemical study, and this concept opens up a potentially new functional paradigm for iron-sulfur centers in iron-dependent enzymes as transient iron binding and shuttling sites to ensure full metal loading of the catalytic site.


  • Organizational Affiliation

    Department of Chemistry, Georgia State University, Atlanta, Georgia 30303; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303. Electronic address: Fangel@uchicago.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyanthranilate 3,4-dioxygenase174Cupriavidus metallidurans CH34Mutation(s): 0 
Gene Names: Cupriavidus metalliduransnbaCRmet_5193
EC: 1.13.11.6
UniProt
Find proteins for Q1LCS4 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Explore Q1LCS4 
Go to UniProtKB:  Q1LCS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1LCS4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.34α = 90
b = 58.34β = 90
c = 231.426γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
MOLREPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description