3EW2

Crystal structure of rhizavidin-biotin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 

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This is version 1.2 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: https://doi.org/10.1016/j.jmb.2008.11.061
  • Primary Citation of Related Structures:  
    3EW1, 3EW2

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
rhizavidin
A, B, C, D, E
A, B, C, D, E, F, G
135Rhizobium etli CFN 42Mutation(s): 0 
Gene Names: RHE_PD00032
UniProt
Find proteins for Q8KKW2 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42))
Explore Q8KKW2 
Go to UniProtKB:  Q8KKW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KKW2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.654α = 90
b = 130.035β = 90
c = 237.555γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations