3EW2

Crystal structure of rhizavidin-biotin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of rhizavidin: insights into the enigmatic high-affinity interaction of an innate biotin-binding protein dimer.

Meir, A.Helppolainen, S.H.Podoly, E.Nordlund, H.R.Hytonen, V.P.Maatta, J.A.Wilchek, M.Bayer, E.A.Kulomaa, M.S.Livnah, O.

(2009) J.Mol.Biol. 386: 379-390

  • DOI: 10.1016/j.jmb.2008.11.061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rhizavidin, from the proteobacterium Rhizobium etli, exhibits high affinity towards biotin but maintains an inherent dimeric quaternary structure and thus, differs from all other known tetrameric avidins. Rhizavidin also differs from the other avidin ...

    Rhizavidin, from the proteobacterium Rhizobium etli, exhibits high affinity towards biotin but maintains an inherent dimeric quaternary structure and thus, differs from all other known tetrameric avidins. Rhizavidin also differs from the other avidins, since it lacks the characteristic tryptophan residue positioned in the L7,8 loop that plays a crucial role in high-affinity binding and oligomeric stability of the tetrameric avidins. The question is, therefore, how does the dimer exist and how is the high biotin-binding affinity retained? For this purpose, the crystal structures of apo- and biotin-complexed rhizavidin were determined. The structures reveal that the rhizavidin monomer exhibits a topology similar to those of other members of the avidin family, that is, eight antiparallel beta-strands that form the conventional avidin beta-barrel. The quaternary structure comprises the sandwich-like dimer, in which the extensive 1-4 intermonomer interface is intact, but the 1-2 and 1-3 interfaces are nonexistent. Consequently, the biotin-binding site is partially accessible, due to the lack of the tryptophan "lid" that distinguishes the tetrameric structures. In rhizavidin, a disulfide bridge connecting the L3,4 and L5,6 loops restrains the L3,4 loop conformation, leaving the binding-site residues essentially unchanged upon biotin binding. Our study suggests that in addition to the characteristic hydrogen bonding and hydrophobic interactions, the preformed architecture of the binding site and consequent shape complementarity play a decisive role in the high-affinity biotin binding of rhizavidin. The structural description of a novel dimeric avidin-like molecule will greatly contribute to the design of improved and unique avidin derivatives for diversifying the capabilities of avidin-biotin technology.


    Organizational Affiliation

    Department of Biological Chemistry, The Institute of Life Sciences, The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Givat Ram, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
rhizavidin
A, B, C, D, E, F, G
135Rhizobium etli (strain CFN 42 / ATCC 51251)Mutation(s): 0 
Find proteins for Q8KKW2 (Rhizobium etli (strain CFN 42 / ATCC 51251))
Go to UniProtKB:  Q8KKW2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTNKd: 215 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 45.654α = 90.00
b = 130.035β = 90.00
c = 237.555γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-10-14 
  • Released Date: 2008-12-23 
  • Deposition Author(s): Livnah, O., Meir, A.

Revision History 

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance