Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78337.12 
• Atom Count: 5422 
• Residue Count: 656 
• Unique protein chains: 1

4GQC

Crystal Structure of Aeropyrum pernix Peroxiredoxin Q Enzyme in Fully-Folded and Locally-Unfolded Conformations

• DOI: 10.2210/pdb4GQC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
• Expression System: Escherichia coli


• Deposited: 2012-08-22 Released: 2012-10-24 
• Deposition Author(s): Perkins, A., Karplus, P.A., Gretes, M.C., Nelson, K.J., Poole, L.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.234 
• R-Value Work: 0.195 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

• 2CX4 - determined by Mizohata, E., Murayama, K., Idaka, M., Tatsuguchi, A., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)  

Literature

Mapping the Active Site Helix-to-Strand Conversion of CxxxxC Peroxiredoxin Q Enzymes.

Perkins, A., Gretes, M.C., Nelson, K.J., Poole, L.B., Karplus, P.A.

(2012) Biochemistry 51: 7638-7650

• PubMed: 22928725 
• DOI: 10.1021/bi301017s
• Primary Citation of Related Structures:  
  4GQF, 4G2E


• PubMed Abstract: 
  

Peroxiredoxins (Prx) make up a family of enzymes that reduce peroxides using a peroxidatic cysteine residue; among these, members of the PrxQ subfamily are proposed to be the most ancestral-like yet are among the least characterized. In many PrxQ enzymes, a second "resolving" cysteine is located five residues downstream from the peroxidatic Cys, and these residues form a disulfide during the catalytic cycle. Here, we describe three hyperthermophilic PrxQ crystal structures originally determined by the RIKEN structural genomics group. We reprocessed the diffraction data and conducted further refinement to yield models with R(free) values lowered by 2.3-7.2% and resolution extended by 0.2-0.3 Å, making one, at 1.4 Å, one of the best resolved peroxiredoxins to date. Comparisons of two matched thiol and disulfide forms reveal that the active site conformational change required for disulfide formation involves a transition of ~20 residues from a pair of α-helices to a β-hairpin and 3(10)-helix. Each conformation has ~10 residues with a high level of disorder providing slack that allows the dramatic shift, and the two conformations are anchored to the protein core by distinct nonpolar side chains that fill three hydrophobic pockets. Sequence conservation patterns confirm the importance of these and a few additional residues for function. From a broader perspective, this study raises the provocative question of how to make use of the valuable information in the Protein Data Bank generated by structural genomics projects but not described in the literature, perhaps remaining unrecognized and certainly underutilized.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Thiol peroxidase	A, B, C, D	164	Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)	Mutation(s): 0  Gene Names: bcp
Find proteins for Q9YA14 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Go to UniProtKB:  Q9YA14

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B, C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DTD	C, D	DITHIANE DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-IMJSIDKUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.234 
• R-Value Work: 0.195 
• Space Group: P 4₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 132.388	α = 90.00
b = 132.388	β = 90.00
c = 106.536	γ = 90.00

Software Package:

Software Name	Purpose
BUSTER	refinement
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-22 
• Released Date: 2012-10-24 
• Deposition Author(s): Perkins, A., Karplus, P.A., Gretes, M.C., Nelson, K.J., Poole, L.B.

Revision History 

• Version 1.0: 2012-10-24
  Type: Initial release
• Version 1.1: 2013-02-20
  Type: Database references