1EH3

R210K N-TERMINAL LOBE HUMAN LACTOFERRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure and iron-binding properties of the R210K mutant of the N-lobe of human lactoferrin: implications for iron release from transferrins.

Peterson, N.A.Anderson, B.F.Jameson, G.B.Tweedie, J.W.Baker, E.N.

(2000) Biochemistry 39: 6625-6633

  • DOI: https://doi.org/10.1021/bi0001224
  • Primary Citation of Related Structures:  
    1EH3

  • PubMed Abstract: 

    Lactoferrin (Lf) and serum transferrin (Tf) combine high-affinity iron binding with an ability to release this iron at reduced pH. Lf, however, retains iron to significantly lower pH than Tf, giving the two proteins distinct functional roles. In this paper, we compared the iron-release profiles for human Lf, Tf, and their N-lobe half-molecules Lf(N) and Tf(N) and showed that half of the difference in iron retention at low pH ( approximately 1.3 pH units) results from interlobe interactions in Lf. To probe factors intrinsic to the N-lobes, we further examined the specific role of two basic residues that are proposed to form a pH-sensitive dilysine trigger for iron release in the N-lobe of Tf [Dewan, J. C., Mikami, B., Hirose, M., and Sacchettini, J. C. (1993) Biochemistry 32, 11963-11968] by mutating Arg 210 to Lys in the N-lobe half-molecule Lf(N). The R210K mutant was expressed, purified, and crystallized, and its crystal structure was determined and refined at 2.0-A resolution to a final R factor (R(free)) of 19.8% (25.0%). The structure showed that Lys 210 and Lys 301 in R210K do not form a dilysine interaction like that between Lys 206 and Lys 296 in human Tf. The R210K mutant retained iron to lower pH than Tf(N), consistent with the absence of the dilysine interaction but released iron at approximately 0.7 pH units higher than Lf(N). We conclude that (i) the ability of Lf to retain iron to significantly lower pH than Tf is due equally to interlobe interactions and to the absence in Lfs of an interaction analogous to the dilysine pair in Tfs, even when two lysines are present at the corresponding sequence positions, and (ii) an appropriately positioned basic residue (Arg 210 in human Lf) modulates iron release by inhibiting protonation of the N-lobe iron ligands, specifically His 253.


  • Organizational Affiliation

    Institute of Molecular Biosciences and Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LACTOFERRIN334Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P02788 (Homo sapiens)
Explore P02788 
Go to UniProtKB:  P02788
PHAROS:  P02788
GTEx:  ENSG00000012223 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02788
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO3
Query on CO3

Download Ideal Coordinates CCD File 
C [auth A]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.44α = 90
b = 57.18β = 117.09
c = 57.34γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.4: 2021-11-03
    Changes: Advisory, Database references, Derived calculations