Ovotransferrin, C-Terminal Lobe, Apo Form

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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This is version 1.4 of the entry. See complete history


Anion-mediated Fe3+ release mechanism in ovotransferrin C-lobe: a structurally identified SO4(2-) binding site and its implications for the kinetic pathway.

Mizutani, K.Muralidhara, B.K.Yamashita, H.Tabata, S.Mikami, B.Hirose, M.

(2001) J Biol Chem 276: 35940-35946

  • DOI: https://doi.org/10.1074/jbc.M102590200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The differential properties of anion-mediated Fe(3+) release between the N- and C-lobes of transferrins have been a focus in transferrin biochemistry. The structural and kinetic characteristics for isolated lobe have, however, been documented with the N-lobe only. Here we demonstrate for the first time the quantitative Fe(3+) release kinetics and the anion-binding structure for the isolated C-lobe of ovotransferrin. In the presence of pyrophosphate, sulfate, and nitrilotriacetate anions, the C-lobe released Fe(3+) with a decelerated rate in a single exponential progress curve, and the observed first order rate constants displayed a hyperbolic profile as a function of the anion concentration. The profile was consistent with a newly derived single-pathway Fe(3+) release model in which the holo form is converted depending on the anion concentration into a "mixed ligand" intermediate that releases Fe(3+). The apo C-lobe was crystallized in ammonium sulfate solution, and the structure determined at 2.3 A resolution demonstrated the existence of a single bound SO(4)(2-) in the interdomain cleft, which interacts directly with Thr(461)-OG1, Tyr(431)-OH, and His(592)-NE2 and indirectly with Tyr(524)-OH. The latter three groups are Fe(3+)-coordinating ligands, strongly suggesting the facilitated Fe(3+) release upon the anion occupation at this site. The SO(4)(2-) binding structure supported the single-pathway kinetic model.

  • Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Uji, Kyoto 611 0011, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ovotransferrin345Gallus gallusMutation(s): 0 
Find proteins for P02789 (Gallus gallus)
Explore P02789 
Go to UniProtKB:  P02789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02789
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
Query on SO4

Download Ideal Coordinates CCD File 
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.58α = 90
b = 81.13β = 90
c = 50.08γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Structure summary