8HNJ

Domain-stabilized glutamine-binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Domain-wise dissection of thermal stability enhancement in multidomain proteins.

Oh, J.Durai, P.Kannan, P.Park, J.Yeon, Y.J.Lee, W.K.Park, K.Seo, M.H.

(2023) Int J Biol Macromol 237: 124141-124141

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.124141
  • Primary Citation of Related Structures:  
    8HNJ

  • PubMed Abstract: 

    Stability is critical for the proper functioning of all proteins. Optimization of protein thermostability is a key step in the development of industrial enzymes and biologics. Herein, we demonstrate that multidomain proteins can be stabilized significantly using domain-based engineering followed by the recombination of the optimized domains. Domain-level analysis of designed protein variants with similar structures but different thermal profiles showed that the independent enhancement of the thermostability of a constituent domain improves the overall stability of the whole multidomain protein. The crystal structure and AlphaFold-predicted model of the designed proteins via domain-recombination provided a molecular explanation for domain-based stepwise stabilization. Our study suggests that domain-based modular engineering can minimize the sequence space for calculations in computational design and experimental errors, thereby offering useful guidance for multidomain protein engineering.


  • Organizational Affiliation

    Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine ABC transporter, periplasmic glutamine-binding protein GlnH
A, B, C, D, E
A, B, C, D, E, F
230Escherichia coli 908519Mutation(s): 0 
Gene Names: HMPREF1604_05361
UniProt
Find proteins for P0AEQ3 (Escherichia coli (strain K12))
Explore P0AEQ3 
Go to UniProtKB:  P0AEQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEQ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 235.1α = 90
b = 69.59β = 90.711
c = 83.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentKorea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release