PDBsum entry: 1hd4

Glycoprotein

PDB id: 1hd4

Contents

Protein chain

92 a.a. *

Ligands

NAG-NAG-BMA-MAN-MAN-NAG-NAG-GAL-GAL

* Residue conservation analysis

PDB id:

1hd4

Name:

Glycoprotein

Title:

Solution structure of the a-subunit of human chorionic gonadotropin [modeled with diantennary glycan at asn78]

Structure:

Chorionic gonadotropin. Chain: a. Other_details: glycosylated at asn52 and asn78

Source:

Homo sapiens. Human. Organism_taxid: 9606. Other_details: isolated from urine of pregnant woman

NMR struc:

26 models

Authors:

P.J.A.Erbel,Y.Karimi-Nejad,J.A.Van Kuik,R.Boelens, J.P.Kamerling,J.F.G.Vliegenthart

Key ref:

P.J.Erbel et al. (2000). Effects of the N-linked glycans on the 3D structure of the free alpha-subunit of human chorionic gonadotropin. Biochemistry, 39, 6012-6021. PubMed id: 10821673 DOI: 10.1021/bi992786n

Date:

07-Nov-00 Release date: 07-Dec-00

Protein chain

P01215  (GLHA_HUMAN) -  Glycoprotein hormones alpha chain

Seq: 116 a.a.

Struc: 92 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (2 terms)
• Biological process: developmental growth (11 terms)
• Biochemical function: hormone activity (1 term)

DOI no: 10.1021/bi992786n

Biochemistry 39:6012-6021 (2000)

PubMed id: 10821673

Effects of the N-linked glycans on the 3D structure of the free alpha-subunit of human chorionic gonadotropin.

P.J.Erbel, Y.Karimi-Nejad, J.A.van Kuik, R.Boelens, J.P.Kamerling, J.F.Vliegenthart.

ABSTRACT

To gain insight into intramolecular carbohydrate-protein interactions at the molecular level, the solution structure of differently deglycosylated variants of the alpha-subunit of human chorionic gonadotropin have been studied by NMR spectroscopy. Significant differences in chemical shifts and NOE intensities were observed for amino acid residues close to the carbohydrate chain at Asn78 upon deglycosylation beyond Asn78-bound GlcNAc. As no straightforward strategy is available for the calculation of the NMR structure of intact glycoproteins, a suitable computational protocol had to be developed. To this end, the X-PLOR carbohydrate force field designed for structure refinement was extended and modified. Furthermore, a computational strategy was devised to facilitate successful protein folding in the presence of extended glycans during the simulation. The values for phi and psi dihedral angles of the glycosidic linkages of the oligosaccharide core fragments GlcNAc2(beta1-4)GlcNAc1 and Man3(beta1-4)GlcNAc2 are restricted to a limited range of the broad conformational energy minima accessible for free glycans. This demonstrates that the protein core affects the dynamic behavior of the glycan at Asn78 by steric hindrance. Reciprocally, the NMR structures indicate that the glycan at Asn78 affects the stability of the protein core. The backbone angular order parameters and displacement data of the generated conformers display especially for the beta-turn 20-23 a decreased structural order upon splitting off the glycan beyond the Asn78-bound GlcNAc. In particular, the Asn-bound GlcNAc shields the protein surface from the hydrophilic environment through interaction with predominantly hydrophobic amino acid residues located in both twisted beta-hairpins consisting of residues 10-28 and 59-84.