1CCF

How an Epidermal Growth Factor (EGF)-Like Domain Binds Calcium-High Resolution NMR Structure of the Calcium Form of the NH2-Terminal EGF-Like Domain in Coagulation Factor X


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

How an epidermal growth factor (EGF)-like domain binds calcium. High resolution NMR structure of the calcium form of the NH2-terminal EGF-like domain in coagulation factor X.

Selander-Sunnerhagen, M.Ullner, M.Persson, E.Teleman, O.Stenflo, J.Drakenberg, T.

(1992) J.Biol.Chem. 267: 19642-19649


  • PubMed Abstract: 
  • Domains homologous to the epidermal growth factor (EGF) are important building blocks for extracellular proteins. Proteins containing these domains have been shown to function in such diverse biological processes as blood coagulation, complement acti ...

    Domains homologous to the epidermal growth factor (EGF) are important building blocks for extracellular proteins. Proteins containing these domains have been shown to function in such diverse biological processes as blood coagulation, complement activation, and the developmental determination of embryonic cell fates. Many of these proteins require calcium for their biological function. In the case of coagulation factors IX and X and anticoagulants proteins C and S, calcium has been found to bind to the EGF-like domains. We have now determined the three-dimensional structure of the calcium-bound form of the NH2-terminal EGF-like domain in coagulation factor X by two-dimensional NMR and simulated folding. Ligands to the calcium ion are the two backbone carbonyls in Gly-47 and Gly-64, as well as the side chains in Gln-49, erythro-beta-hydroxyaspartic acid (Hya) 63, and possibly Asp-46. The conserved Asp-48 is not a ligand in our present structures. The remaining ligands are assumed to be solvent molecules or, in the intact protein, ligands from neighboring domains. Other proteins interacting in a calcium-dependent manner may also contribute ligands. A comparison with the calcium-free form shows that calcium binding induces strictly local structural changes in the domain. Residues corresponding to the side chain ligands in factor X are conserved in many other proteins, such as the integral membrane protein TAN-1 of human lymphocytes and its developmentally important homolog, Notch, in Drosophila. Calcium binding to EGF-like domains may be crucial for numerous protein-protein interactions involving EGF-like domains in coagulation factors, plasma proteins, and membrane proteins. Therefore, there is reason to believe that this novel calcium site plays an important role in the biochemistry of extracellular proteins.


    Related Citations: 
    • Calcium Binding to the Isolated Beta-Hydroxyaspartic Acid-Containing Epidermal Growth Factor-Like Domain of the Bovine Factor X
      Selander, M.,Persson, E.,Drakenberg, T.,Linse, S.
      (1989) J.Biol.Chem. 264: 16897
    • Three-Dimensional Structure of the Apo Form of the N-Terminal Egf-Like Module of Blood Coagulation Factor X as Determined by NMR Spectroscopy and Simulated Folding
      Ullner, M.,Selander, M.,Persson, E.,Stenflo, J.,Teleman, O.,Drakenberg, T.
      (1992) Biochemistry 31: 5974
    • 1H NMR Assignment and Secondary Structure of the Ca2+-Free Form of the Amino-Terminal Epidermal Growth Factor Like Domain in Coagulation Factor X
      Selander, M.,Persson, E.,Stenflo, J.,Drakenberg, T.
      (1990) Biochemistry 29: 8111


    Organizational Affiliation

    Department of Physical Chemistry 2, University of Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR X
A
42Bos taurusGene Names: F10
EC: 3.4.21.6
Find proteins for P00743 (Bos taurus)
Go to Gene View: F10
Go to UniProtKB:  P00743
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BH2
Query on BH2
A
L-PEPTIDE LINKINGC4 H7 N O5ASP
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 15 
  • Olderado: 1CCF Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 2.0: 2017-08-16
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Polymer sequence, Structure summary