6IWR

Crystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of carbohydrate transfer activity of UDP-GalNAc: Polypeptide N-acetylgalactosaminyltransferase 7.

Yu, C.Liang, L.Yin, Y.

(2019) Biochem Biophys Res Commun 510: 266-271

  • DOI: 10.1016/j.bbrc.2019.01.084
  • Primary Citation of Related Structures:  
    6IWQ, 6IWR

  • PubMed Abstract: 
  • The UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) catalyze mucin-type O-glycosylation by transferring α-N-acetylgalactosamine (GalNAc) from UDP- GalNAc to Ser or Thr residues of target proteins. We resolved the crystal structures of GalNAc-T7, a GalNAc-T capable of glycosylating consecutive sites, and of its complex with the donor substrate UDP-GalNAc ...

    The UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) catalyze mucin-type O-glycosylation by transferring α-N-acetylgalactosamine (GalNAc) from UDP- GalNAc to Ser or Thr residues of target proteins. We resolved the crystal structures of GalNAc-T7, a GalNAc-T capable of glycosylating consecutive sites, and of its complex with the donor substrate UDP-GalNAc. The N-terminal catalytic domain and C-terminal lectin domain are connected by a flexible linker, forming a narrow cleft for the acceptor substrate. Only the α subdomain of the lectin domain binds to the glycosyl group, indicating that key residues determine substrate binding. Compared to the Apo structure, the loop covering the catalytic center of the complex show significant conformational changes, indicating the mechanism of the catalytic reaction.


    Organizational Affiliation

    Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China. Electronic address: yinyuxin@hsc.pku.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-acetylgalactosaminyltransferase 7A, B, C, D, E, F597Homo sapiensMutation(s): 0 
Gene Names: GALNT7
EC: 2.4.1 (PDB Primary Data), 2.4.1.41 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86SF2 (Homo sapiens)
Explore Q86SF2 
Go to UniProtKB:  Q86SF2
PHAROS:  Q86SF2
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.435α = 90
b = 158.264β = 90
c = 251.484γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-12-06 
  • Released Date: 2019-02-06 
  • Deposition Author(s): Yu, C., Yin, Y.X.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary