Crystal structure of apo AVR4 (R112L,C122S)

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester.

Hayouka, R.Eisenberg-Domovich, Y.Hytonen, V.P.Maatta, J.A.Nordlund, H.R.Kulomaa, M.S.Wilchek, M.Bayer, E.A.Livnah, O.

(2008) Acta Crystallogr D Biol Crystallogr 64: 302-308

  • DOI: https://doi.org/10.1107/S0907444907067844
  • Primary Citation of Related Structures:  
    2OF8, 2OF9, 2OFA, 2OFB

  • PubMed Abstract: 

    The homotetrameric and biotin-binding properties of avidin and streptavidin have been exploited for a myriad of biotechnological applications and theoretical studies. Among the few differences between the two proteins is the capacity of avidin to hydrolyze biotinyl p-nitrophenyl ester (BNP), as opposed to streptavidin, which fully protects the same pseudosubstrate from hydrolysis. Combined mutagenesis and X-ray analysis have been used to attempt to understand this diametric difference in activities. It was found that a charged residue and one of the loops (L3,4) are together responsible for this difference. Recently, the avidin-related analogue AVR4 was found to have an even more pronounced BNP-hydrolysis activity than avidin. Again, the combination of charged residue(s) (Asp39 and/or Arg112) and the rigid conformation of the L3,4 loop was suggested to be responsible for the observed hydrolysis reaction. However, replacement of the latter charged residues in AVR4 resulted in only a modest reduction in hydrolytic activity at most, whereas replacement of the L3,4 loop of avidin with the rigid loop of AVR4 caused a dramatic increase in the activity of avidin. These results clearly demonstrate that the main feature responsible for the observed differences in rates of hydrolysis among the avidins is the conformational status of the L3,4 loop, which imposes conformational constraints on the pseudosubstrate, thereby rendering it susceptible to nucleophilic attack by solvent. In this context, the hydrolytic properties of the avidins reflect enzyme catalysis, in that subtleties in substrate binding are the determining features of catalytic efficiency.

  • 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, Jerusalem 91904, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Avidin-related protein 4/5
A, B
126Gallus gallusMutation(s): 2 
Gene Names: AVR4
Find proteins for P56734 (Gallus gallus)
Explore P56734 
Go to UniProtKB:  P56734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56734
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.852α = 90
b = 77.852β = 90
c = 110.782γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-12-27
    Changes: Data collection