7C87

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) C50S/F80C/C207S/C213S mutant (ApPrx*F80C)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.156 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rebuilding Ring-Type Assembly of Peroxiredoxin by Chemical Modification.

Himiyama, T.Tsuchiya, Y.Yonezawa, Y.Nakamura, T.

(2021) Bioconjug Chem 32: 153-160

  • DOI: https://doi.org/10.1021/acs.bioconjchem.0c00587
  • Primary Citation of Related Structures:  
    7C87, 7C89, 7C8A, 7CQJ

  • PubMed Abstract: 

    Direct control of the protein quaternary structure (QS) is challenging owing to the complexity of the protein structure. As a protein with a characteristic QS, peroxiredoxin from Aeropyrum pernix K1 (ApPrx) forms a decamer, wherein five dimers associate to form a ring. Here, we disrupted and reconstituted ApPrx QS via amino acid mutations and chemical modifications targeting hot spots for protein assembly. The decameric QS of an ApPrx* mutant, wherein all cysteine residues in wild-type ApPrx were mutated to serine, was destructed to dimers via an F80C mutation. The dimeric ApPrx*F80C mutant was then modified with a small molecule and successfully assembled as a decamer. Structural analysis confirmed that an artificially installed chemical moiety potentially facilitates suitable protein-protein interactions to rebuild a native structure. Rebuilding of dodecamer was also achieved through an additional amino acid mutation. This study describes a facile method to regulate the protein assembly state.


  • Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxiredoxin
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
250Aeropyrum pernix K1Mutation(s): 4 
Gene Names: APE_2278
EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for Q9Y9L0 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9Y9L0 
Go to UniProtKB:  Q9Y9L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y9L0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
K [auth A]
L [auth B]
M [auth C]
N [auth D]
O [auth E]
K [auth A],
L [auth B],
M [auth C],
N [auth D],
O [auth E],
P [auth F],
Q [auth G],
R [auth H],
S [auth I],
T [auth J]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.156 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.065α = 106.026
b = 103.134β = 104.752
c = 104.956γ = 92.595
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19K21133
Japan Society for the Promotion of Science (JSPS)Japan20K15403

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Derived calculations, Refinement description