2KEQ | pdb_00002keq

Solution structure of DnaE intein from Nostoc punctiforme

• PDB DOI: https://doi.org/10.2210/pdb2KEQ/pdb

• Classification: SPLICING
• Organism(s): Nostoc punctiforme PCC 73102
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-02 Released: 2009-05-19 
• Deposition Author(s): Oeemig, J.S., Aranko, A.S., Djupsj, J.B., Iwai, H.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification.

Oeemig, J.S., Aranko, A.S., Djupsjobacka, J., Heinamaki, K., Iwai, H.

(2009) FEBS Lett 583: 1451-1456

• PubMed: 19344715 
• DOI: https://doi.org/10.1016/j.febslet.2009.03.058
• Primary Citation Related Structures: 
  2KEQ


• PubMed Abstract: 
  

  Naturally split DnaE intein from Nostoc punctiforme (Npu) has robust protein trans-splicing activity and high tolerance of sequence variations at the splicing junctions. We determined the solution structure of a single chain variant of NpuDnaE intein by NMR spectroscopy. Based on the NMR structure and the backbone dynamics of the single chain NpuDnaE intein, we designed a functional split variant of the NpuDnaE intein having a short C-terminal half (C-intein) composed of six residues. In vivo and in vitro protein ligation of model proteins by the newly designed split intein were demonstrated.

---

Organizational Affiliation: 
• Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FIN-00014, Finland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.93 kDa 
• Atom Count: 1,119 
• Modeled Residue Count: 139 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III alpha subunit, Nucleic acid binding OB-fold tRNA/helicase-type	A	139	Nostoc punctiforme PCC 73102	Mutation(s): 1  Gene Names: DnaE, Npun_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
UniProt Groups	B2J066B2J821

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-19 
Deposition Author(s): Oeemig, J.S., Aranko, A.S., Djupsj, J.B., Iwai, H.

Revision History  

• Version 1.0: 2009-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-05-29
  Changes: Data collection