4MPS

Crystal structure of rat Beta-galactoside alpha-2,6-sialyltransferase 1 (ST6GAL1), Northeast Structural Genomics Consortium Target RnR367A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzymatic Basis for N-Glycan Sialylation: STRUCTURE OF RAT alpha 2,6-SIALYLTRANSFERASE (ST6GAL1) REVEALS CONSERVED AND UNIQUE FEATURES FOR GLYCAN SIALYLATION.

Meng, L.Forouhar, F.Thieker, D.Gao, Z.Ramiah, A.Moniz, H.Xiang, Y.Seetharaman, J.Milaninia, S.Su, M.Bridger, R.Veillon, L.Azadi, P.Kornhaber, G.Wells, L.Montelione, G.T.Woods, R.J.Tong, L.Moremen, K.W.

(2013) J.Biol.Chem. 288: 34680-34698

  • DOI: 10.1074/jbc.M113.519041

  • PubMed Abstract: 
  • Glycan structures on glycoproteins and glycolipids play critical roles in biological recognition, targeting, and modulation of functions in animal systems. Many classes of glycan structures are capped with terminal sialic acid residues, which contrib ...

    Glycan structures on glycoproteins and glycolipids play critical roles in biological recognition, targeting, and modulation of functions in animal systems. Many classes of glycan structures are capped with terminal sialic acid residues, which contribute to biological functions by either forming or masking glycan recognition sites on the cell surface or secreted glycoconjugates. Sialylated glycans are synthesized in mammals by a single conserved family of sialyltransferases that have diverse linkage and acceptor specificities. We examined the enzymatic basis for glycan sialylation in animal systems by determining the crystal structures of rat ST6GAL1, an enzyme that creates terminal α2,6-sialic acid linkages on complex-type N-glycans, at 2.4 Å resolution. Crystals were obtained from enzyme preparations generated in mammalian cells. The resulting structure revealed an overall protein fold broadly resembling the previously determined structure of pig ST3GAL1, including a CMP-sialic acid-binding site assembled from conserved sialylmotif sequence elements. Significant differences in structure and disulfide bonding patterns were found outside the sialylmotif sequences, including differences in residues predicted to interact with the glycan acceptor. Computational substrate docking and molecular dynamics simulations were performed to predict and evaluate the CMP-sialic acid donor and glycan acceptor interactions, and the results were compared with kinetic analysis of active site mutants. Comparisons of the structure with pig ST3GAL1 and a bacterial sialyltransferase revealed a similar positioning of donor, acceptor, and catalytic residues that provide a common structural framework for catalysis by the mammalian and bacterial sialyltransferases.


    Organizational Affiliation

    From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-galactoside alpha-2,6-sialyltransferase 1
A, B
310Rattus norvegicusMutation(s): 0 
Gene Names: St6gal1
Find proteins for G3V680 (Rattus norvegicus)
Go to UniProtKB:  G3V680
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 134.720α = 90.00
b = 49.754β = 92.30
c = 86.063γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXphasing
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-11-06
    Type: Database references
  • Version 1.2: 2013-12-25
    Type: Database references