1VZM

OSTEOCALCIN FROM FISH ARGYROSOMUS REGIUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Evidence of a Fourth Gla Residue in Fish Osteocalcin: Biological Implications

Frazao, C.Simes, D.C.Coelho, R.Alves, D.Williamson, M.K.Price, P.A.Cancela, M.L.Carrondo, M.A.

(2005) Biochemistry 44: 1234

  • DOI: 10.1021/bi048336z

  • PubMed Abstract: 
  • Osteocalcin is a small (45 amino acids) secreted protein found to accumulate in bone and dentin of many organisms by interacting with calcium and hydroxyapatite, through the presence of three gamma-carboxylated residues. In this work, we describe the ...

    Osteocalcin is a small (45 amino acids) secreted protein found to accumulate in bone and dentin of many organisms by interacting with calcium and hydroxyapatite, through the presence of three gamma-carboxylated residues. In this work, we describe the first X-ray crystal structure for a nonmammalian osteocalcin, obtained at 1.4 A resolution, purified from the marine teleost fish Argyrosomus regius. The three-dimensional fit between the A. regius structure and that of the only other known X-ray structure, the porcine osteocalcin, revealed a superposition of the Calpha atoms of their metal chelating residues, Gla and Asp, showing that their spatial distribution is consistent with the interatomic distances of calcium cations in the hydroxyapatite crystals. In both structures, the protein forms a tight globular arrangement of their three alpha-helices while the remaining residues, at N- and C-terminal regions, have essentially no secondary structure characteristics. This study revealed the presence of a fourth gamma-carboxylation at Glu(25), not previously detected in the structure of the porcine osteocalcin or in any other of the sequentially characterized mammalian osteocalcins (human, cow, and rat). A confirmation of the fourth Gla residue in A. regius osteocalcin was achieved via LC-MS analysis. These four doubly charged residues are, together with Asp(24), concentrated in a common surface region located on the same side of the molecule. This further suggests that the known high affinity of osteocalcin for bone mineral may be derived from the clustering of calcium binding sites on this surface of the molecules.


    Related Citations: 
    • Purification of Matrix Gla Protein from a Marine Teleost Fish, Argyrosomus Regius: Calcified Cartilage and not Bone as the Primary Site of Mgp Accumulation in Fish
      Simes, D.C.,Williamson, M.K.,Ortiz-Delgado, J.B.,Viegas, C.S.,Price, P.A.,Cancela, M.L.
      (2003) J.Bone Miner.Res. 18: 244


    Organizational Affiliation

    ITQB-UNL, Av. da Rep├║blica, 2784-505 Oeiras, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OSTEOCALCIN
A, B, C
45Argyrosomus regiusMutation(s): 0 
Gene Names: bglap
Find proteins for Q800Y1 (Argyrosomus regius)
Go to UniProtKB:  Q800Y1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
A, B, C
L-PEPTIDE LINKINGC6 H9 N O6GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.700α = 90.00
b = 48.700β = 90.00
c = 119.100γ = 120.00
Software Package:
Software NamePurpose
SHELXDphasing
SHELXL-97refinement
SCALEPACKdata scaling
SHELXCDphasing
SHELXEphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation, Other