6RYM

Structure of carbohydrate recognition domain with GlcNAc bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Atomic-resolution crystal structures of the immune protein conglutinin from cow reveal specific interactions of its binding site withN-acetylglucosamine.

Paterson, J.M.Shaw, A.J.Burns, I.Dodds, A.W.Prasad, A.Reid, K.B.Greenhough, T.J.Shrive, A.K.

(2019) J Biol Chem 294: 17155-17165

  • DOI: 10.1074/jbc.RA119.010271
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bovine conglutinin is an immune protein that is involved in host resistance to microbes and parasites and interacts with complement component iC3b, agglutinates erythrocytes, and neutralizes influenza A virus. Here, we determined the high-resolution ...

    Bovine conglutinin is an immune protein that is involved in host resistance to microbes and parasites and interacts with complement component iC3b, agglutinates erythrocytes, and neutralizes influenza A virus. Here, we determined the high-resolution (0.97-1.46 Å) crystal structures with and without bound ligand of a recombinant fragment of conglutinin's C-terminal carbohydrate-recognition domain (CRD). The structures disclosed that the high-affinity ligand N -acetyl-d-glucosamine (GlcNAc) binds in the collectin CRD calcium site by interacting with the O3' and O4' hydroxyls alongside additional specific interactions of the N -acetyl group oxygen and nitrogen with Lys-343 and Asp-320, respectively. These residues, unique to conglutinin and differing both in sequence and in location from those in other collectins, result in specific, high-affinity binding for GlcNAc. The binding pocket flanking residue Val-339, unlike the equivalent Arg-343 in the homologous human surfactant protein D, is sufficiently small to allow conglutinin Lys-343 access to the bound ligand, whereas Asp-320 lies in an extended loop proximal to the ligand-binding site and bounded at both ends by conserved residues that coordinate to both calcium and ligand. This loop becomes ordered on ligand binding. The electron density revealed both α and β anomers of GlcNAc, consistent with the added α/βGlcNAc mixture. Crystals soaked with α1-2 mannobiose, a putative component of iC3b, reported to bind to conglutinin, failed to reveal bound ligand, suggesting a requirement for presentation of mannobiose as part of an extended physiological ligand. These results reveal a highly specific GlcNAc-binding pocket in conglutinin and a novel collectin mode of carbohydrate recognition.


    Organizational Affiliation

    School of Life Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom a.k.shrive@keele.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Conglutinin
A
128Bos taurusMutation(s): 0 
Gene Names: CGN1
Find proteins for P23805 (Bos taurus)
Go to UniProtKB:  P23805
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.225α = 90
b = 50.225β = 90
c = 51.925γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references