6SNH

Cryo-EM structure of yeast ALG6 in complex with 6AG9 Fab and Dol25-P-Glc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanism of the ER-based glucosyltransferase ALG6.

Bloch, J.S.Pesciullesi, G.Boilevin, J.Nosol, K.Irobalieva, R.N.Darbre, T.Aebi, M.Kossiakoff, A.A.Reymond, J.L.Locher, K.P.

(2020) Nature 579: 443-447

  • DOI: 10.1038/s41586-020-2044-z
  • Primary Citation of Related Structures:  
    6SNH, 6SNI

  • PubMed Abstract: 
  • In eukaryotic protein N-glycosylation, a series of glycosyltransferases catalyse the biosynthesis of a dolichylpyrophosphate-linked oligosaccharide before its transfer onto acceptor proteins 1 . The final seven steps occur in the lumen of the endoplasmic reticulum (ER) and require dolichylphosphate-activated mannose and glucose as donor substrates 2 ...

    In eukaryotic protein N-glycosylation, a series of glycosyltransferases catalyse the biosynthesis of a dolichylpyrophosphate-linked oligosaccharide before its transfer onto acceptor proteins 1 . The final seven steps occur in the lumen of the endoplasmic reticulum (ER) and require dolichylphosphate-activated mannose and glucose as donor substrates 2 . The responsible enzymes-ALG3, ALG9, ALG12, ALG6, ALG8 and ALG10-are glycosyltransferases of the C-superfamily (GT-Cs), which are loosely defined as containing membrane-spanning helices and processing an isoprenoid-linked carbohydrate donor substrate 3,4 . Here we present the cryo-electron microscopy structure of yeast ALG6 at 3.0 Å resolution, which reveals a previously undescribed transmembrane protein fold. Comparison with reported GT-C structures suggests that GT-C enzymes contain a modular architecture with a conserved module and a variable module, each with distinct functional roles. We used synthetic analogues of dolichylphosphate-linked and dolichylpyrophosphate-linked sugars and enzymatic glycan extension to generate donor and acceptor substrates using purified enzymes of the ALG pathway to recapitulate the activity of ALG6 in vitro. A second cryo-electron microscopy structure of ALG6 bound to an analogue of dolichylphosphate-glucose at 3.9 Å resolution revealed the active site of the enzyme. Functional analysis of ALG6 variants identified a catalytic aspartate residue that probably acts as a general base. This residue is conserved in the GT-C superfamily. Our results define the architecture of ER-luminal GT-C enzymes and provide a structural basis for understanding their catalytic mechanisms.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland. locher@mol.biol.ethz.ch.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferaseA [auth X]562Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ALG6YOR002WUNA544
EC: 2.4.1.267
Membrane Entity: Yes 
UniProt
Find proteins for Q12001 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12001 
Go to UniProtKB:  Q12001
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12001
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
6AG9 Fab heavy chainB [auth H]234synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
6AG9 Fab light chainC [auth L]217synthetic constructMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LMH (Subject of Investigation/LOI)
Query on LMH

Download Ideal Coordinates CCD File 
D [auth X]glucosyl-dolichol phosphate
C31 H55 O9 P
AGLXCEGQRIYVRV-HAYNYTLHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandCRSII3_147632
Swiss National Science FoundationSwitzerlandCRSII5_173709
Swiss National Science FoundationSwitzerland310030B_166672

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2020-04-01
    Changes: Database references