8I76 | pdb_00008i76

Crystal structure of decarboxylated osteocalcin at pH 2.0 without glycerol

• PDB DOI: https://doi.org/10.2210/pdb8I76/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-31 Released: 2024-01-31 
• Deposition Author(s): Yokoyama, T., Nabeshima, Y., Obita, T., Mizuguchi, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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

• PubMed: 36976525 
• DOI: https://doi.org/10.1002/1873-3468.14618
• Primary Citation 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.

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Organizational Affiliation: 
• Faculty of Pharmaceutical Sciences, University of Toyama, Toyama, Japan.
Division of Functional Structure, Department of Morphological Biology, Fukuoka Dental College, Fukuoka, Japan.
Oral Medicine Research Center, Fukuoka Dental College, Fukuoka, Japan.
Department of Applied Chemistry and Bioscience, Chitose Institute of Science and Technology (CIST), Chitose, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.5 kDa 
• Atom Count: 590 
• Modeled Residue Count: 62 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Osteocalcin	A, B	38	Bos taurus	Mutation(s): 0  Gene Names: BGLAP
UniProt
Find proteins for P02820 (Bos taurus) Explore P02820  Go to UniProtKB:  P02820

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.105	α = 90
b = 42.105	β = 90
c = 36.711	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Yokoyama, T., Nabeshima, Y., Obita, T., Mizuguchi, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release
  
• Version 1.1: 2024-08-21
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary