9HTH | pdb_00009hth

Crystal structure of the fused, cysteine-less Aes123 PolB1 split intein (with S1A, N159A mutations)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 
    0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A cysteine-less and ultra-fast split intein rationally engineered from being aggregation-prone to highly efficient in protein trans-splicing.

Humberg, C.Yilmaz, Z.Fitzian, K.Dorner, W.Kummel, D.Mootz, H.D.

(2025) Nat Commun 16: 2723-2723

  • DOI: https://doi.org/10.1038/s41467-025-57596-x
  • Primary Citation of Related Structures:  
    9HTH

  • PubMed Abstract: 

    Split inteins catalyze protein trans-splicing by ligating their extein sequences while undergoing self-excision, enabling diverse protein modification applications. However, many purified split intein precursors exhibit partial or no splicing activity for unknown reasons. The Aes123 PolB1 intein, a representative of the rare cysteine-less split inteins, is of particular interest due to its resistance to oxidative conditions and orthogonality to thiol chemistries. In this work, we identify β-sheet-dominated aggregation of its N-terminal intein fragment as the origin of its low (~30%) splicing efficiency. Using computational, biochemical, and biophysical analyses, we characterize the fully active monomeric fraction and pinpoint aggregation-prone regions. Supported by a crystal structure, we design stably monomeric mutants with nearly complete splicing activity. The optimized CLm intein (Cysteine-Less and monomeric) retains the wild-type's ultra-fast reaction rate and serves as an efficient, thiol-independent protein modification tool. We find that other benchmark split inteins show similar precursor aggregation, suggesting that this general phenomenon arises from the intrinsic challenge to maintain the precursor in a partially disordered state while promoting stable folding upon fragment association.


  • Organizational Affiliation

    Institute of Biochemistry, University of Münster, Corrensstraße 36, 48149, Münster, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed DNA polymerase
A, B
173Aeromonas phage Aes123Mutation(s): 1 
EC: 2.7.7.7
UniProt
Find proteins for I6YMS9 (Aeromonas phage Aes123)
Explore I6YMS9 
Go to UniProtKB:  I6YMS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6YMS9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free:  0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.129α = 90
b = 63.013β = 90
c = 162.404γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyDFG MO1073/9-1

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release