2NXV

Structure of the 6th ORF of the Rhodobacter blastica ATPase operon; Majastridin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a protein, structurally related to glycosyltransferases, encoded in the Rhodobacter blasticus atp operon.

Enroth, C.Strid, A.

(2008) Biochim.Biophys.Acta 1784: 379-384

  • DOI: 10.1016/j.bbapap.2007.11.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The F1-ATP synthase atp operon in the proteobacterium Rhodobacter blasticus contains six open reading frames, encoding six hypothetical proteins. Five of these subunits, in the stoichiometry (alphabeta)3gamma delta epsilon make up the catalytic F1-AT ...

    The F1-ATP synthase atp operon in the proteobacterium Rhodobacter blasticus contains six open reading frames, encoding six hypothetical proteins. Five of these subunits, in the stoichiometry (alphabeta)3gamma delta epsilon make up the catalytic F1-ATP synthase complex similarly in bacteria, chloroplasts and mitochondria. The sixth gene of the R. blasticus atp operon, urf6, shows very little sequence homology to any protein of known structure or function. The gene has previously been cloned, the product (called majastridin) has been heterologously expressed in Escherichia coli, and purified to high homogeneity [M. Brosché, I. Kalbina, M. Arnfelt, G. Benito, B.G. Karlsson, A. Strid, Occurrence, overexpression and partial purification of the protein (majastridin) corresponding to the URF6 gene of the Rhodobacter blasticus atp operon, Eur. J. Biochem. 255 (1998) 87-92]. We have solved the X-ray crystal structure and refined a model of majastridin to atomic resolution. Here we present the crystal structures of apo-majastridin and the complex of majastridin with Mn2+ and UDP and show that it has extensive structural similarity to glycosyltransferases (EC 2.4). This is the first structure determined from a new group of distantly related bacterial proteins of at least six members. They share the identical amino acids that bind Mn2+ and a triplet of amino acids in the putative sugar-binding site.


    Organizational Affiliation

    Department of Science and Orebro Life Science Center, Orebro University, SE-70182 Orebro, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunits region ORF 6
A, B
249Rhodobacter blasticusMutation(s): 0 
Find proteins for P05449 (Rhodobacter blasticus)
Go to UniProtKB:  P05449
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
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: 1.1 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.137 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 121.873α = 90.00
b = 90.311β = 90.00
c = 69.590γ = 90.00
Software Package:
Software NamePurpose
SHELXSphasing
PDB_EXTRACTdata extraction
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-20 
  • Released Date: 2007-12-18 
  • Deposition Author(s): Enroth, C., Strid, A.

Revision History 

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2018-03-07
    Type: Data collection