6E7I

Human ppGalNAcT2 I253A/L310A Mutant with EA2 and UDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells.

Schumann, B.Malaker, S.A.Wisnovsky, S.P.Debets, M.F.Agbay, A.J.Fernandez, D.Wagner, L.J.S.Lin, L.Li, Z.Choi, J.Fox, D.M.Peh, J.Gray, M.A.Pedram, K.Kohler, J.J.Mrksich, M.Bertozzi, C.R.

(2020) Mol Cell 78: 824-834.e15

  • DOI: https://doi.org/10.1016/j.molcel.2020.03.030
  • Primary Citation of Related Structures:  
    6E7I, 6NQT

  • PubMed Abstract: 

    Studying posttranslational modifications classically relies on experimental strategies that oversimplify the complex biosynthetic machineries of living cells. Protein glycosylation contributes to essential biological processes, but correlating glycan structure, underlying protein, and disease-relevant biosynthetic regulation is currently elusive. Here, we engineer living cells to tag glycans with editable chemical functionalities while providing information on biosynthesis, physiological context, and glycan fine structure. We introduce a non-natural substrate biosynthetic pathway and use engineered glycosyltransferases to incorporate chemically tagged sugars into the cell surface glycome of the living cell. We apply the strategy to a particularly redundant yet disease-relevant human glycosyltransferase family, the polypeptide N-acetylgalactosaminyl transferases. This approach bestows a gain-of-chemical-functionality modification on cells, where the products of individual glycosyltransferases can be selectively characterized or manipulated to understand glycan contribution to major physiological processes.


  • Organizational Affiliation

    Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom. Electronic address: b.schumann@imperial.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polypeptide N-acetylgalactosaminyltransferase 2535Homo sapiensMutation(s): 2 
Gene Names: GALNT2
EC: 2.4.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q10471 (Homo sapiens)
Explore Q10471 
Go to UniProtKB:  Q10471
PHAROS:  Q10471
GTEx:  ENSG00000143641 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10471
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EA2B [auth P]13Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q62605 (Rattus norvegicus)
Explore Q62605 
Go to UniProtKB:  Q62605
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62605
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
C [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.31α = 90
b = 69.31β = 90
c = 169.78γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesNIH R01 CA200423

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description