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: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1074/jbc.M113.519041
  • Primary Citation of Related Structures:  
    4MPS

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactoside alpha-2,6-sialyltransferase 1
A, B
310Rattus norvegicusMutation(s): 0 
Gene Names: rCG_36561St6gal1
EC: 2.4.99.1
UniProt
Find proteins for P13721 (Rattus norvegicus)
Explore P13721 
Go to UniProtKB:  P13721
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13721
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.72α = 90
b = 49.754β = 92.3
c = 86.063γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2013-12-25
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary