4O1R

Crystal structure of NpuDnaB intein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based engineering and comparison of novel split inteins for protein ligation.

Aranko, A.S.Oeemig, J.S.Zhou, D.Kajander, T.Wlodawer, A.Iwai, H.

(2014) Mol Biosyst 10: 1023-1034

  • DOI: 10.1039/c4mb00021h
  • Primary Citation of Related Structures:  4O1S

  • PubMed Abstract: 
  • Protein splicing is an autocatalytic process involving self-excision of an internal protein domain, the intein, and concomitant ligation of the two flanking sequences, the exteins, with a peptide bond. Protein splicing can also take place in trans by ...

    Protein splicing is an autocatalytic process involving self-excision of an internal protein domain, the intein, and concomitant ligation of the two flanking sequences, the exteins, with a peptide bond. Protein splicing can also take place in trans by naturally split inteins or artificially split inteins, ligating the exteins on two different polypeptide chains into one polypeptide chain. Protein trans-splicing could work in foreign contexts by replacing the native extein sequences with other protein sequences. Protein ligation using protein trans-splicing increasingly becomes a useful tool for biotechnological applications such as semi-synthesis of proteins, segmental isotopic labeling, and in vivo protein engineering. However, only a few split inteins have been successfully applied for protein ligation. Naturally split inteins have been widely used, but they are cross-reactive to each other, limiting their applications to multiple-fragment ligation. Based on the three-dimensional structures including two newly determined intein structures, we derived 21 new split inteins from four highly efficient cis-splicing inteins, in order to develop novel split inteins suitable for protein ligation. We systematically compared trans-splicing of 24 split inteins and tested the cross-activities among them to identify orthogonal split intein fragments that could be used in chemical biology and biotechnological applications.


    Organizational Affiliation

    Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki, FIN-00014, Finland. hideo.iwai@helsinki.fi.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replicative DNA helicase
A
142Nostoc punctiforme (strain ATCC 29133 / PCC 73102)EC: 3.6.4.12
Find proteins for B2IVH9 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102))
Go to UniProtKB:  B2IVH9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.161 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.054α = 90.00
b = 61.054β = 90.00
c = 122.179γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Refinement description, Source and taxonomy