Crystal structure of Megavirus UDP-GlcNAc 4,6-dehydratase, 5-epimerase Mg534

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Giant Virus Megavirus chilensis Encodes the Biosynthetic Pathway for Uncommon Acetamido Sugars.

Piacente, F.De Castro, C.Jeudy, S.Molinaro, A.Salis, A.Damonte, G.Bernardi, C.Abergel, C.Tonetti, M.G.

(2014) J Biol Chem 289: 24428-24439

  • DOI: https://doi.org/10.1074/jbc.M114.588947
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Giant viruses mimicking microbes, by the sizes of their particles and the heavily glycosylated fibrils surrounding their capsids, infect Acanthamoeba sp., which are ubiquitous unicellular eukaryotes. The glycans on fibrils are produced by virally encoded enzymes, organized in gene clusters. Like Mimivirus, Megavirus glycans are mainly composed of virally synthesized N-acetylglucosamine (GlcNAc). They also contain N-acetylrhamnosamine (RhaNAc), a rare sugar; the enzymes involved in its synthesis are encoded by a gene cluster specific to Megavirus close relatives. We combined activity assays on two enzymes of the pathway with mass spectrometry and NMR studies to characterize their specificities. Mg534 is a 4,6-dehydratase 5-epimerase; its three-dimensional structure suggests that it belongs to a third subfamily of inverting dehydratases. Mg535, next in the pathway, is a bifunctional 3-epimerase 4-reductase. The sequential activity of the two enzymes leads to the formation of UDP-l-RhaNAc. This study is another example of giant viruses performing their glycan synthesis using enzymes different from their cellular counterparts, raising again the question of the origin of these pathways.

  • Organizational Affiliation

    From the Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV,1 16132 Genova, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative dTDP-d-glucose 4 6-dehydratase323Megavirus chiliensisMutation(s): 0 
Gene Names: mg534
Find proteins for G5CSR9 (Megavirus chiliensis)
Explore G5CSR9 
Go to UniProtKB:  G5CSR9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG5CSR9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
C21 H30 N7 O17 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.509α = 90
b = 153.509β = 90
c = 60.68γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-09-10
    Changes: Database references
  • Version 2.0: 2020-03-11
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description