PDBsum entry: 1q3m

Calcium-binding protein

PDB id: 1q3m

Contents

Protein chain

34 a.a. *

* Residue conservation analysis

PDB id:

1q3m

Name:

Calcium-binding protein

Title:

1h nmr structure bundle of bovine ca2+-osteocalcin

Structure:

Osteocalcin. Chain: a. Synonym: gamma-carboxyglutamic acid-containing protein, bone gla-protein, bgp

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Other_details: bone powder

NMR struc:

13 models

Authors:

T.L.Dowd,J.F.Rosen,L.Li,C.M.Gundberg

Key ref:

T.L.Dowd et al. (2003). The three-dimensional structure of bovine calcium ion-bound osteocalcin using 1H NMR spectroscopy. Biochemistry, 42, 7769-7779. PubMed id: 12820886 DOI: 10.1021/bi034470s

Date:

30-Jul-03 Release date: 16-Sep-03

Protein chain

P02820  (OSTCN_BOVIN) -  Osteocalcin

Seq: 100 a.a.

Struc: 34 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: regulation of bone mineralization (1 term)
• Biochemical function: calcium ion binding (1 term)

DOI no: 10.1021/bi034470s

Biochemistry 42:7769-7779 (2003)

PubMed id: 12820886

The three-dimensional structure of bovine calcium ion-bound osteocalcin using 1H NMR spectroscopy.

T.L.Dowd, J.F.Rosen, L.Li, C.M.Gundberg.

ABSTRACT

Structural information on osteocalcin or other noncollagenous bone proteins is very limited. We have solved the three-dimensional structure of calcium bound osteocalcin using (1)H 2D NMR techniques and proposed a mechanism for mineral binding. The protons in the 49 amino acid sequence were assigned using standard two-dimensional homonuclear NMR experiments. Distance constraints, dihedral angle constraints, hydrogen bonds, and (1)H and (13)C chemical shifts were all used to calculate a family of 13 structures. The tertiary structure of the protein consisted of an unstructured N terminus and a C-terminal loop (residues 16-49) formed by long-range hydrophobic interactions. Elements of secondary structure within residues 16-49 include type III turns (residues 20-25) and two alpha-helical regions (residues 27-35 and 41-44). The three Gla residues project from the same face of the helical turns and are surface exposed. The genetic algorithm-molecular dynamics simulation approach was used to place three calcium atoms on the NMR-derived structure. One calcium atom was coordinated by three side chain oxygen atoms, two from Asp30, and one from Gla24. The second calcium atom was coordinated to four oxygen atoms, two from the side chain in Gla 24, and two from the side chain of Gla 21. The third calcium atom was coordinated to two oxygen atoms of the side chain of Gla17. The best correlation of the distances between the uncoordinated Gla oxygen atoms is with the intercalcium distance of 9.43 A in hydroxyapatite. The structure may provide further insight into the function of osteocalcin.