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Journal of molecular biology1999; 289(2); 303-317; doi: 10.1006/jmbi.1999.2767

Three-dimensional structure of mare diferric lactoferrin at 2.6 A resolution.

Abstract: Lactoferrin is a monomeric glycoprotein with a molecular mass of approximately 80 kDa. The three-dimensional structure of mare diferric lactoferrin (mlf) has been determined at 2.6 A resolution. The protein crystallizes in the space group P 212121with a=85.2 A, b=99.5 A, c=103.1 A with a solvent content of 55 % (v/v). The structure was solved by the molecular replacement method using human diferric lactoferrin as the model. The structure has been refined using XPLOR to a final R -factor of 0.194 for all data in the 15-2.6 A resolution range. The amino acid sequence of mlf was determined using a cDNA method. The final refined model comprises 5281 protein atoms, 2 Fe3+, 2 CO32-and 112 water molecules. The overall folding of mlf is similar to that of other proteins of the transferrin family. The protein folds into two globular lobes, N and C. The lobes are further divided into two domains, N1 and N2, and C1 and C2. The iron-binding cleft is situated between the domains in each lobe. The N lobe appears to be well ordered and is more stable than the C lobe in mlf unlike in other lactoferrins, where the C lobe is the more stable. The opening of the binding cleft in the N lobe of mlf is narrower than those in other proteins of the transferrin family. This is very unusual and is found only in mare lactoferrin. Apart from certain hydrophobic interactions at the mouth of the cleft, one salt-bridge (Lys301 . . . . . . . . Glu216) crosses between the two walls of the cleft. The two lobes are connected covalently by a three-turn alpha-helix involving residues 334-344. The N lobe displays a highly ordered structure with appreciably low temperature factors. The iron coordination is more symmetrical in the N lobe than in the C lobe. There are only 16 intermolecular hydrogen bonds in the structure of mlf.
Copyright 1999 Academic Press.
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Publication Date: 1999-06-15 PubMed ID: 10366507DOI: 10.1006/jmbi.1999.2767Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The study presents the 3D structure of mare diferric lactoferrin, a glycoprotein determined using X-ray crystallography. The protein is found to share structural similarities with other transferrin family proteins but with distinct features such as a narrower binding cleft and unusual stability of the N lobe.

Detailed Explanation

  • This research focuses on the three-dimensional structure of mare diferric lactoferrin (mlf), a monomeric glycoprotein identified in mammals, primarily in many exocrine secretions like milk and tears. Lactoferrin carries out various biological roles, including iron binding and providing immunity. The associated molecular mass is around 80 kDa.
  • The researchers crystallized the protein under investigation, with the crystal existing in the space group P 212121. The unit cell dimensions were a=85.2 A, b=99.5 A, c=103.1 A and the solvent content was 55 % v/v. The crystallization provided a matrix that allowed the study of protein structure in detail through diffraction methods.
  • The structure of the mlf was then solved using the molecular replacement method, a technique that places a known, similar structure into the unit cell of the crystal to provide a starting model for analysis. In this case, human diferric lactoferrin was used as the model.
  • The refined model of the protein was then obtained through a series of computational operations to fit the experimental data. The refinement process used XPLOR software and concluded with a final R -factor (statistical measure used to assess the fit between the observed and calculated structure factor amplitudes) of 0.194 for all data in the resolution range of 15 to 2.6 A (angstrom).
  • The obtained protein structure is folded into two globular lobes, labeled N and C. Each lobe is further divided into two smaller domains, N1 and N2, and C1 and C2. The iron-binding cleft, an important space where iron ions bind, is found between the domains in each lobe.
  • One peculiar feature of mlf, unlike other lactoferrins, is that the N lobe is more stable than the C lobe. Moreover, the opening of the binding cleft in the N lobe is narrower than those found in other transferrin family proteins.
  • The two lobes are connected covalently by a three-turn alpha-helix, a common secondary structure in proteins, involving amino acid residues 334-344. The iron coordination is found to be more symmetrical in the stable N lobe compared to the C lobe.
  • The structure comprises only 16 intermolecular hydrogen bonds, significantly shaping the protein’s final three-dimensional structure.

Cite This Article

APA
Sharma AK, Paramasivam M, Srinivasan A, Yadav MP, Singh TP. (1999). Three-dimensional structure of mare diferric lactoferrin at 2.6 A resolution. J Mol Biol, 289(2), 303-317. https://doi.org/10.1006/jmbi.1999.2767

Publication

Journal of molecular biology
ISSN: 0022-2836
NlmUniqueID: 2985088R
Country: Netherlands
Language: English
Volume: 289
Issue: 2
Pages: 303-317

Researcher Affiliations

Sharma, A K
  • Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110 029, India.
Paramasivam, M
    Srinivasan, A
      Yadav, M P
        Singh, T P

          MeSH Terms

          • Amino Acid Sequence
          • Animals
          • Base Sequence
          • Computer Graphics
          • Crystallography, X-Ray
          • Female
          • Horses
          • Humans
          • Hydrogen Bonding
          • Lactoferrin / chemistry
          • Lactoferrin / genetics
          • Models, Molecular
          • Molecular Sequence Data
          • Protein Folding
          • Protein Structure, Secondary
          • Software

          Citations

          This article has been cited 18 times.
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          9. Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access. Proteomics 2015 Jul;15(14):2525-46.
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          12. Sharma S, Sinha M, Kaushik S, Kaur P, Singh TP. C-lobe of lactoferrin: the whole story of the half-molecule. Biochem Res Int 2013;2013:271641.
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          13. Golla K, Cherukuvada B, Ahmed F, Kondapi AK. Efficacy, safety and anticancer activity of protein nanoparticle-based delivery of doxorubicin through intravenous administration in rats. PLoS One 2012;7(12):e51960.
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            doi: 10.1021/acsomega.3c06560pubmed: 37970015google scholar: lookup
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