2N8N

Solution structure of translation initiation factor


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and dynamics study of translation initiation factor 1 from Staphylococcus aureus suggests its RNA binding mode

Kim, D.H.Kang, S.J.Lee, K.Y.Jang, S.B.Kang, S.M.Lee, B.J.

(2017) Biochim.Biophys.Acta 1865: 65-75

  • DOI: 10.1016/j.bbapap.2016.10.009

  • PubMed Abstract: 
  • Translation initiation, the rate-limiting step in the protein synthesis, is tightly regulated. As one of the translation initiation factors, translation initiation factor 1 (IF1) plays crucial roles not only in translation but also in many cellular p ...

    Translation initiation, the rate-limiting step in the protein synthesis, is tightly regulated. As one of the translation initiation factors, translation initiation factor 1 (IF1) plays crucial roles not only in translation but also in many cellular processes that are important for genomic stability, such as the activity of RNA chaperones. Here, we characterize the RNA interactions and dynamics of IF1 from Staphylococcus aureus Mu50 (IF1 Sa ) by NMR spectroscopy. First, the NMR-derived solution structure of IF1 Sa revealed that IF1 Sa adopts an oligonucleotide/oligosaccharide binding (OB)-fold. Structural comparisons showed large deviations in the α-helix and the following loop, which are potential RNA-binding regions of the OB-fold, as well as differences in the electrostatic potential surface among bacterial IF1s. Second, the 15 N NMR relaxation data for IF1 Sa indicated the flexible nature of the α-helix and the following loop region of IF1 Sa . Third, RNA-binding properties were studied using FP assays and NMR titrations. FP binding assays revealed that IF1 Sa binds to RNAs with moderate affinity. In combination with the structural analysis, the NMR titration results revealed the RNA binding sites. Taken together, these results show that IF1 Sa binds RNAs with moderate binding affinity via the residues that occupy the large surface area of its β-barrel. These findings suggest that IF1 Sa is likely to bind RNA in various conformations rather than only at a specific site and indicate that the flexible RNA binding mode of IF1 Sa is necessary for its interaction with various RNA substrates.


    Organizational Affiliation

    The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea. Electronic address: lbj@nmr.snu.ac.kr.,The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Translation initiation factor IF-1
A
72Staphylococcus aureus (strain Mu50 / ATCC 700699)Mutation(s): 0 
Gene Names: infA
Find proteins for P65118 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P65118
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-21 
  • Released Date: 2016-10-26 
  • Deposition Author(s): Kim, D., Lee, K., Lee, B.

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references