7EVF

Plant growth-promoting factor YxaL mutant from Bacillus velezensis - T175W/S213G/W215A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structure of the plant growth-promoting factor YxaL from the rhizobacterium Bacillus velezensis and its application to protein engineering.

Kim, J.Pham, H.Baek, Y.Jo, I.Kim, Y.H.Ha, N.C.

(2022) Acta Crystallogr D Struct Biol 78: 104-112

  • DOI: https://doi.org/10.1107/S2059798321011724
  • Primary Citation of Related Structures:  
    7DXN, 7EQ5, 7EVF

  • PubMed Abstract: 

    The YxaL protein was isolated from the soil bacterium Bacillus velezensis and has been shown to promote the root growth of symbiotic plants. YxaL has further been suggested to act as an exogenous signaling protein to induce the growth and branching of plant roots. Amino acid sequence analysis predicted YxaL to exhibit an eight-bladed β-propeller fold stabilized by six tryptophan-docking motifs and two modified motifs. Protein engineering to improve its structural stability is needed to increase the utility of YxaL as a plant growth-promoting factor. Here, the crystal structure of YxaL from B. velezensis was determined at 1.8 Å resolution to explore its structural features for structure-based protein engineering. The structure showed the typical eight-bladed β-propeller fold with structural variations in the third and fourth blades, which may decrease the stability of the β-propeller fold. Engineered proteins targeting the modified motifs were subsequently created. Crystal structures of the engineered YxaL proteins showed that the typical tryptophan-docking interaction was restored in the third and fourth blades, with increased structural stability, resulting in improved root growth-promoting activity in Arabidopsis seeds. The work is an example of structure-based protein engineering to improve the structural stability of β-propellor fold proteins.


  • Organizational Affiliation

    Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Sciences, CALS, Seoul National University, Seoul 08826, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PQQ_3 domain-containing proteinA [auth AA]373Bacillus velezensis FZB42Mutation(s): 4 
Gene Names: RBAM_036900
UniProt
Find proteins for A7ZAJ3 (Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42))
Explore A7ZAJ3 
Go to UniProtKB:  A7ZAJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7ZAJ3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.987α = 90
b = 152.987β = 90
c = 61.694γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description