1WBI

AVR2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Avidin Related Protein 2 Shows Unique Structural and Functional Features Among the Avidin Protein Family.

Hytonen, V.P.Maatta, J.A.Kidron, H.Halling, K.K.Horha, J.Kulomaa, T.Nyholm, T.K.M.Johnson, M.S.Salminen, T.A.Kulomaa, M.S.Airenne, T.T.

(2005) BMC Biotechnol 5: 28

  • DOI: https://doi.org/10.1186/1472-6750-5-28
  • Primary Citation of Related Structures:  
    1WBI

  • PubMed Abstract: 

    The chicken avidin gene family consists of avidin and several avidin related genes (AVRs). Of these gene products, avidin is the best characterized and is known for its extremely high affinity for D-biotin, a property that is utilized in numerous modern life science applications. Recently, the AVR genes have been expressed as recombinant proteins, which have shown different biotin-binding properties as compared to avidin. In the present study, we have employed multiple biochemical methods to better understand the structure-function relationship of AVR proteins focusing on AVR2. Firstly, we have solved the high-resolution crystal structure of AVR2 in complex with a bound ligand, D-biotin. The AVR2 structure reveals an overall fold similar to the previously determined structures of avidin and AVR4. Major differences are seen, especially at the 1-3 subunit interface, which is stabilized mainly by polar interactions in the case of AVR2 but by hydrophobic interactions in the case of AVR4 and avidin, and in the vicinity of the biotin binding pocket. Secondly, mutagenesis, competitive dissociation analysis and differential scanning calorimetry were used to compare and study the biotin-binding properties as well as the thermal stability of AVRs and avidin. These analyses pinpointed the importance of residue 109 for biotin binding and stability of AVRs. The I109K mutation increased the biotin-binding affinity of AVR2, whereas the K109I mutation decreased the biotin-binding affinity of AVR4. Furthermore, the thermal stability of AVR2(I109K) increased in comparison to the wild-type protein and the K109I mutation led to a decrease in the thermal stability of AVR4. Altogether, this study broadens our understanding of the structural features determining the ligand-binding affinities and stability as well as the molecular evolution within the protein family. This novel information can be applied to further develop and improve the tools already widely used in avidin-biotin technology.


  • Organizational Affiliation

    NanoScience Center, Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (YAB), FI-40014, Finland. veshyto@bytl.jyu.fi


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AVIDIN-RELATED PROTEIN 2
A, B, C, D, E
A, B, C, D, E, F, G, H
129Gallus gallusMutation(s): 0 
UniProt
Find proteins for P56732 (Gallus gallus)
Explore P56732 
Go to UniProtKB:  P56732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56732
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTN
Query on BTN

Download Ideal Coordinates CCD File 
EA [auth G]
HA [auth H]
I [auth A]
N [auth B]
R [auth C]
EA [auth G],
HA [auth H],
I [auth A],
N [auth B],
R [auth C],
V [auth D],
W [auth E],
Z [auth F]
BIOTIN
C10 H16 N2 O3 S
YBJHBAHKTGYVGT-ZKWXMUAHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth F]
FA [auth G]
GA [auth G]
IA [auth H]
CA [auth F],
DA [auth F],
FA [auth G],
GA [auth G],
IA [auth H],
JA [auth H],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
T [auth C],
U [auth C],
X [auth E],
Y [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
J [auth A]
O [auth B]
P [auth B]
AA [auth F],
BA [auth F],
J [auth A],
O [auth B],
P [auth B],
S [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.669α = 90
b = 99.936β = 90
c = 135.191γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description