1XHB | pdb_00001xhb

The Crystal Structure of UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferase-T1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.255 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

The beginnings of mucin biosynthesis: The crystal structure of UDP-GalNAc:polypeptide {alpha}-N-acetylgalactosaminyltransferase-T1

Fritz, T.A.Hurley, J.H.Trinh, L.B.Shiloach, J.Tabak, L.A.

(2004) Proc Natl Acad Sci U S A 101: 15307-15312

  • DOI: https://doi.org/10.1073/pnas.0405657101
  • Primary Citation Related Structures: 
    1XHB

  • PubMed Abstract: 

    UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferases (ppGaNTases) initiate the formation of mucin-type, O-linked glycans by catalyzing the transfer of alpha-N-acetylgalactosamine from UDP-GalNAc to Ser or Thr residues of core proteins to form the Tn antigen (GalNAc-alpha-1-O-Ser/Thr). ppGaNTases are unique among glycosyltransferases in containing a C-terminal lectin domain. We present the x-ray crystal structure of a ppGaNTase, murine ppGaNTase-T1, and show that it folds to form distinct catalytic and lectin domains. The association of the two domains forms a large cleft in the surface of the enzyme that contains a Mn2+ ion complexed by invariant D209 and H211 of the "DXH" motif and by invariant H344. Each of the three potential lectin domain carbohydrate-binding sites (alpha, beta, and gamma) is located on the active-site face of the enzyme, suggesting a mechanism by which the transferase may accommodate multiple conformations of glycosylated acceptor substrates. A model of a mucin 1 glycopeptide substrate bound to the enzyme shows that the spatial separation between the lectin alpha site and a modeled active site UDP-GalNAc is consistent with the in vitro pattern of glycosylation observed for this peptide catalyzed by ppGaNTase-T1. The structure also provides a template for the larger ppGaNTase family, and homology models of several ppGaNTase isoforms predict dramatically different surface chemistries consistent with isoform-selective acceptor substrate recognition.


  • Organizational Affiliation
    • Section on Biological Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 54.96 kDa 
  • Atom Count: 3,695 
  • Modeled Residue Count: 447 
  • Deposited Residue Count: 472 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polypeptide N-acetylgalactosaminyltransferase 1472Mus musculusMutation(s): 0 
Gene Names: Galnt1
EC: 2.4.1.41
UniProt
Find proteins for O08912 (Mus musculus)
Explore O08912 
Go to UniProtKB:  O08912
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08912
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O08912-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.255 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.605α = 90
b = 65.605β = 90
c = 125.947γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Structure summary