6XFI | pdb_00006xfi

Crystal Structures of beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2): Structural Basis for Inherited Muscular Dystrophies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.227 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

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Literature

Crystal structures of beta-1,4-N-acetylglucosaminyltransferase 2: structural basis for inherited muscular dystrophies.

Yang, J.Y.Halmo, S.M.Praissman, J.Chapla, D.Singh, D.Wells, L.Moremen, K.W.Lanzilotta, W.N.

(2021) Acta Crystallogr D Struct Biol 77: 486-495

  • DOI: https://doi.org/10.1107/S2059798321001261
  • Primary Citation Related Structures: 
    6XFI, 6XI2

  • PubMed Abstract: 

    The canonical O-mannosylation pathway in humans is essential for the functional glycosylation of α-dystroglycan. Disruption of this post-translational modification pathway leads to congenital muscular dystrophies. The first committed step in the construction of a functional matriglycan structure involves the post-translational modification of α-dystroglycan. This is essential for binding extracellular matrix proteins and arenaviruses, and is catalyzed by β-1,4-N-acetylglucosaminyltransferase 2 (POMGNT2). While another glycosyl transferase, β-1,4-N-acetylglucosaminyltransferase 1 (POMGNT1), has been shown to be promiscuous in extending O-mannosylated sites, POMGNT2 has been shown to display significant primary amino-acid selectivity near the site of O-mannosylation. Moreover, several single point mutations in POMGNT2 have been identified in patients with assorted dystroglycanopathies such as Walker-Warburg syndrome and limb girdle muscular dystrophy. To gain insight into POMGNT2 function in humans, the enzyme was expressed as a soluble, secreted fusion protein by transient infection of HEK293 suspension cultures. Here, crystal structures of POMGNT2 (amino-acid residues 25-580) with and without UDP bound are reported. Consistent with a novel fold and a unique domain organization, no molecular-replacement model was available and phases were obtained through crystallization of a selenomethionine variant of the enzyme in the same space group. Tetragonal (space group P42 1 2; unit-cell parameters a = b = 129.8, c = 81.6 Å, α = γ = β = 90°) crystals with UDP bound diffracted to 1.98 Å resolution and contained a single monomer in the asymmetric unit. Orthorhombic (space group P2 1 2 1 2 1 ; unit-cell parameters a = 142.3, b = 153.9, c = 187.4 Å, α = γ = β = 90°) crystals were also obtained; they diffracted to 2.57 Å resolution and contained four monomers with differential glycosylation patterns and conformations. These structures provide the first rational basis for an explanation of the loss-of-function mutations and offer significant insights into the mechanics of this important human enzyme.


  • Organizational Affiliation
    • The Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.

Macromolecule Content 

  • Total Structure Weight: 61.88 kDa 
  • Atom Count: 4,480 
  • Modeled Residue Count: 511 
  • Deposited Residue Count: 529 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2529Homo sapiensMutation(s): 0 
Gene Names: POMGNT2AGO61C3orf39EOGTLGTDC2
EC: 2.4.1.312
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NAT1 (Homo sapiens)
Explore Q8NAT1 
Go to UniProtKB:  Q8NAT1
PHAROS:  Q8NAT1
GTEx:  ENSG00000144647 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NAT1
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q8NAT1-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.227 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.84α = 90
b = 129.84β = 90
c = 81.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111939-05

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-21
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary