2QTX

Crystal structure of an Hfq-like protein from Methanococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An Hfq-like protein in archaea: Crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii.

Nielsen, J.S.Boggild, A.Andersen, C.B.Nielsen, G.Boysen, A.Brodersen, D.E.Valentin-Hansen, P.

(2007) Rna 13: 2213-2223

  • DOI: 10.1261/rna.689007

  • PubMed Abstract: 
  • The Sm and Sm-like proteins are conserved in all three domains of life and have emerged as important players in many different RNA-processing reactions. Their proposed role is to mediate RNA-RNA and/or RNA-protein interactions. In marked contrast to ...

    The Sm and Sm-like proteins are conserved in all three domains of life and have emerged as important players in many different RNA-processing reactions. Their proposed role is to mediate RNA-RNA and/or RNA-protein interactions. In marked contrast to eukaryotes, bacteria appear to contain only one distinct Sm-like protein belonging to the Hfq family of proteins. Similarly, there are generally only one or two subtypes of Sm-related proteins in archaea, but at least one archaeon, Methanococcus jannaschii, encodes a protein that is related to Hfq. This archaeon does not contain any gene encoding a conventional archaeal Sm-type protein, suggesting that Hfq proteins and archaeal Sm-homologs can complement each other functionally. Here, we report the functional characterization of M. jannaschii Hfq and its crystal structure at 2.5 A resolution. The protein forms a hexameric ring. The monomer fold, as well as the overall structure of the complex is similar to that found for the bacterial Hfq proteins. However, clear differences are seen in the charge distribution on the distal face of the ring, which is unusually negative in M. jannaschii Hfq. Moreover, owing to a very short N-terminal alpha-helix, the overall diameter of the archaeal Hfq hexamer is significantly smaller than its bacterial counterparts. Functional analysis reveals that Escherichia coli and M. jannaschii Hfqs display very similar biochemical and biological properties. It thus appears that the archaeal and bacterial Hfq proteins are largely functionally interchangeable.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein MJ1435
A, B, C, D, E, F, G, H, I, J, K, L
71Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Find proteins for Q58830 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58830
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.866α = 90.00
b = 67.110β = 104.03
c = 119.064γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling
RESOLVEphasing
HKL-2000data reduction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description