2C1Q | pdb_00002c1q

X-ray structure of biotin binding protein from chicken


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.220 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structure and Characterization of a Novel Chicken Biotin-Binding Protein a (Bbp-A).

Hytonen, V.P.Maatta, J.A.E.Niskanen, E.A.Huuskonen, J.Helttunen, K.J.Halling, K.K.Nordlund, H.R.Rissanen, K.Johnson, M.S.Salminen, T.A.Kulomaa, M.S.Laitinen, O.H.Airenne, T.T.

(2007) BMC Struct Biol 7: 8

  • DOI: https://doi.org/10.1186/1472-6807-7-8
  • Primary Citation Related Structures: 
    2C1Q, 2C1S

  • PubMed Abstract: 

    The chicken genome contains a BBP-A gene showing similar characteristics to avidin family genes. In a previous study we reported that the BBP-A gene may encode a biotin-binding protein due to the high sequence similarity with chicken avidin, especially at regions encoding residues known to be located at the ligand-binding site of avidin. Here, we expand the repertoire of known macromolecular biotin binders by reporting a novel biotin-binding protein A (BBP-A) from chicken. The BBP-A recombinant protein was expressed using two different expression systems and purified with affinity chromatography, biochemically characterized and two X-ray structures were solved - in complex with D-biotin (BTN) and in complex with D-biotin D-sulfoxide (BSO). The BBP-A protein binds free biotin with high, "streptavidin-like" affinity (Kd ~ 10-13 M), which is about 50 times lower than that of chicken avidin. Surprisingly, the affinity of BBP-A for BSO is even higher than the affinity for BTN. Furthermore, the solved structures of the BBP-A--BTN and BBP-A--BSO complexes, which share the fold with the members of the avidin and lipocalin protein families, are extremely similar to each other. BBP-A is an avidin-like protein having a beta-barrel fold and high affinity towards BTN. However, BBP-A differs from the other known members of the avidin protein family in thermal stability and immunological properties. BBP-A also has a unique ligand-binding property, the ability to bind BTN and BSO at comparable affinities. BBP-A may have use as a novel material in, e.g. modern bio(nano)technological applications.


  • Organizational Affiliation
    • NanoScience Center, Department of Biological and Environmental Science, P.O. Box 35 (YAB), FI-40014 University of Jyväskylä, Finland. veshyto@mat.ethz.ch <veshyto@mat.ethz.ch>

Macromolecule Content 

  • Total Structure Weight: 14.36 kDa 
  • Atom Count: 1,052 
  • Modeled Residue Count: 123 
  • Deposited Residue Count: 126 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BIOTIN BINDING PROTEIN A126Gallus gallusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.220 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.653α = 90
b = 61.653β = 90
c = 179.659γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-20
    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: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary