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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1074/jbc.M115.650259
  • Primary Citation of Related Structures:  

  • 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 cellul ...

    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

    From the Department of Chemistry, Center for Diagnostics and Therapeutics, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-hydroxyanthranilate 3,4-dioxygenase
A
174Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)Mutation(s): 0 
Gene Names: nbaC
EC: 1.13.11.6
Find proteins for Q1LCS4 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34))
Go to UniProtKB:  Q1LCS4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.340α = 90.00
b = 58.340β = 90.00
c = 231.426γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SERGUIdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-06-04 
  • Released Date: 2015-05-06 
  • Deposition Author(s): Liu, F., Liu, A.

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-07-15
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description
  • Version 1.3: 2019-07-17
    Type: Data collection, Refinement description