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PDBsum entry 2keq

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protein links
Splicing PDB id
2keq
Jmol
Contents
Protein chain
139 a.a. *
* Residue conservation analysis
PDB id:
2keq
Name: Splicing
Title: Solution structure of dnae intein from nostoc punctiforme
Structure: DNA polymerase iii alpha subunit, nucleic acid binding ob-fold tRNA/helicase-type. Chain: a. Engineered: yes. Mutation: yes. Other_details: fusion protein of n-intein part from DNA polymerase iii alpha subunit (residues 1-102) and c-intein part from nucleic acid binding ob-fold, tRNA/helicase-type (residues 103-137)
Source: Nostoc punctiforme pcc 73102. Organism_taxid: 63737. Gene: dnae, npun_f4872. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: J.S.Oeemig,A.S.Aranko,J.B.Djupsj,H.Iwai
Key ref: J.S.Oeemig et al. (2009). Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification. FEBS Lett, 583, 1451-1456. PubMed id: 19344715 DOI: 10.1016/j.febslet.2009.03.058
Date:
02-Feb-09     Release date:   19-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
B2J066  (B2J066_NOSP7) -  DNA polymerase III, alpha subunit
Seq:
Struc:
 
Seq:
Struc:
876 a.a.
139 a.a.*
Protein chain
Pfam   ArchSchema ?
B2J821  (B2J821_NOSP7) -  Nucleic acid binding, OB-fold, tRNA/helicase-type
Seq:
Struc:
 
Seq:
Struc:
450 a.a.
139 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.7.7.7  - DNA-directed Dna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Deoxynucleoside triphosphate
+ DNA(n)
= diphosphate
+ DNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     intein-mediated protein splicing   1 term 

 

 
    reference    
 
 
DOI no: 10.1016/j.febslet.2009.03.058 FEBS Lett 583:1451-1456 (2009)
PubMed id: 19344715  
 
 
Solution structure of DnaE intein from Nostoc punctiforme: structural basis for the design of a new split intein suitable for site-specific chemical modification.
J.S.Oeemig, A.S.Aranko, J.Djupsjöbacka, K.Heinämäki, H.Iwaï.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20820635 G.Volkmann, and H.Iwaï (2010).
Protein trans-splicing and its use in structural biology: opportunities and limitations.
  Mol Biosyst, 6, 2110-2121.  
20203672 M.Muona, A.S.Aranko, V.Raulinaitis, and H.Iwaï (2010).
Segmental isotopic labeling of multi-domain and fusion proteins by protein trans-splicing in vivo and in vitro.
  Nat Protoc, 5, 574-587.  
20449740 S.Elleuche, and S.Pöggeler (2010).
Inteins, valuable genetic elements in molecular biology and biotechnology.
  Appl Microbiol Biotechnol, 87, 479-489.  
20495572 S.Frutos, M.Goger, B.Giovani, D.Cowburn, and T.W.Muir (2010).
Branched intermediate formation stimulates peptide bond cleavage in protein splicing.
  Nat Chem Biol, 6, 527-533.  
19708049 H.D.Mootz (2009).
Split inteins as versatile tools for protein semisynthesis.
  Chembiochem, 10, 2579-2589.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.