3HY2

Crystal Structure of Sulfiredoxin in Complex with Peroxiredoxin I and ATP:Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Protein Engineering of the Quaternary Sulfiredoxin-Peroxiredoxin Enzyme-Substrate Complex Reveals the Molecular Basis for Cysteine Sulfinic Acid Phosphorylation

Jonsson, T.J.Johnson, L.C.Lowther, W.T.

(2009) J.Biol.Chem. 284: 33305-33310

  • DOI: 10.1074/jbc.M109.036400

  • PubMed Abstract: 
  • Oxidative stress can damage the active site cysteine of the antioxidant enzyme peroxiredoxin (Prx) to the sulfinic acid form, Prx-SO(2)(-). This modification leads to inactivation. Sulfiredoxin (Srx) utilizes a unique ATP-Mg(2+)-dependent mechanism t ...

    Oxidative stress can damage the active site cysteine of the antioxidant enzyme peroxiredoxin (Prx) to the sulfinic acid form, Prx-SO(2)(-). This modification leads to inactivation. Sulfiredoxin (Srx) utilizes a unique ATP-Mg(2+)-dependent mechanism to repair the Prx molecule. Using selective protein engineering that involves disulfide bond formation and site-directed mutagenesis, a mimic of the enzyme.substrate complex has been trapped. Here, we present the 2.1 A crystal structure of human Srx in complex with PrxI, ATP, and Mg(2+). The Cys(52) sulfinic acid moiety was substituted by mutating this residue to Asp, leading to a replacement of the sulfur atom with a carbon atom. Because the Srx reaction cannot occur, the structural changes in the Prx active site that lead to the attack on ATP may be visualized. The local unfolding of the helix containing C52D resulted in the packing of Phe(50) in PrxI within a hydrophobic pocket of Srx. Importantly, this structural rearrangement positioned one of the oxygen atoms of Asp(52) within 4.3 A of the gamma-phosphate of ATP bound to Srx. These observations support a mechanism where phosphorylation of Prx-SO(2)(-) is the first chemical step.


    Organizational Affiliation

    Center for Structural Biology and Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxiredoxin-1
A, B
206Homo sapiensGene Names: PRDX1 (PAGA, PAGB, TDPX2)
EC: 1.11.1.15
Find proteins for Q06830 (Homo sapiens)
Go to Gene View: PRDX1
Go to UniProtKB:  Q06830
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sulfiredoxin-1
X, Y
110Homo sapiensGene Names: SRXN1 (C20orf139, SRX)
EC: 1.8.98.2
Find proteins for Q9BYN0 (Homo sapiens)
Go to Gene View: SRXN1
Go to UniProtKB:  Q9BYN0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
X, Y
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.330α = 90.00
b = 92.410β = 90.00
c = 131.850γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
REFMACrefinement
d*TREKdata scaling
PHASERphasing
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-09-18
    Type: Derived calculations