4KL5

Crystal structure of NpuDnaE intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Intermolecular domain swapping induces intein-mediated protein alternative splicing.

Aranko, A.S.Oeemig, J.S.Kajander, T.Iwai, H.

(2013) Nat Chem Biol 9: 616-622

  • DOI: 10.1038/nchembio.1320
  • Primary Citation of Related Structures:  
    4KL5, 4KL6

  • PubMed Abstract: 
  • Protein sequences are diversified on the DNA level by recombination and mutation and can be further increased on the RNA level by alternative RNA splicing, involving introns that have important roles in many biological processes. The protein version of introns (inteins), which catalyze protein splicing, were first reported in the 1990s ...

    Protein sequences are diversified on the DNA level by recombination and mutation and can be further increased on the RNA level by alternative RNA splicing, involving introns that have important roles in many biological processes. The protein version of introns (inteins), which catalyze protein splicing, were first reported in the 1990s. The biological roles of protein splicing still remain elusive because inteins neither provide any clear benefits nor have an essential role in their host organisms. We now report protein alternative splicing, in which new protein sequences can be produced by protein recombination by intermolecular domain swapping of inteins, as elucidated by NMR spectroscopy and crystal structures. We demonstrate that intein-mediated protein alternative splicing could be a new strategy to increase protein diversity (that is, functions) without any modification in genetic backgrounds. We also exploited it as a post-translational protein conformation-driven switch of protein functions (for example, as highly specific protein interference).


    Organizational Affiliation

    Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III, alpha subunit, Nucleic acid binding, OB-fold, tRNA/helicase-type chimeric constructA, B144Nostoc punctiforme PCC 73102Mutation(s): 4 
Gene Names: DnaE N- and C-intein partNpun_F4872
EC: 2.7.7.7
UniProt
Find proteins for B2J066 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2J066 
Go to UniProtKB:  B2J066
Find proteins for B2J821 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Explore B2J821 
Go to UniProtKB:  B2J821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsB2J066B2J821
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.555α = 90
b = 66.7β = 90
c = 67.486γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2014-06-11
    Changes: Derived calculations
  • Version 1.3: 2017-08-09
    Changes: Advisory, Refinement description, Source and taxonomy