8I76

Crystal structure of decarboxylated osteocalcin at pH 2.0 without glycerol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Literature

Structural and mutational analyses of decarboxylated osteocalcin provide insight into its adiponectin-inducing activity.

Mizuguchi, M.Yokoyama, T.Otani, T.Kuribara, S.Nabeshima, Y.Obita, T.Hirata, M.Kawano, K.

(2023) FEBS Lett 597: 1479-1488

  • DOI: https://doi.org/10.1002/1873-3468.14618
  • Primary Citation of Related Structures:  
    8I74, 8I75, 8I76

  • PubMed Abstract: 

    An acidic environment in bone is essential for bone metabolism and the production of decarboxylated osteocalcin, which functions as a regulatory hormone of glucose metabolism. Here, we describe the high-resolution X-ray crystal structure of decarboxylated osteocalcin under acidic conditions. Decarboxylated osteocalcin at pH 2.0 retains the α-helix structure of native osteocalcin with three γ-carboxyglutamic acid residues at neutral pH. This implies that decarboxylated osteocalcin is stable under an acidic environment in bone. In addition, site-directed mutagenesis revealed that Glu17 and Glu21 are important for the adiponectin-inducing activity of decarboxylated osteocalcin. These findings suggest that the receptor of decarboxylated osteocalcin responds to the negative charge in helix 1 of osteocalcin.


  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Osteocalcin
A, B
38Bos taurusMutation(s): 0 
Gene Names: BGLAP
UniProt
Find proteins for P02820 (Bos taurus)
Explore P02820 
Go to UniProtKB:  P02820
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02820
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.105α = 90
b = 42.105β = 90
c = 36.711γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-31
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Database references