6IWR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 structu ...

    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.,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.,Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylgalactosaminyltransferase 7
A, B, C, D, E, F
597Homo sapiensMutation(s): 0 
Gene Names: GALNT7
EC: 2.4.1.41
Find proteins for Q86SF2 (Homo sapiens)
Go to Gene View: GALNT7
Go to UniProtKB:  Q86SF2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
UD2
Query on UD2

Download SDF File 
Download CCD File 
D
URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE
(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C17 H27 N3 O17 P2
LFTYTUAZOPRMMI-NESSUJCYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 137.435α = 90.00
b = 158.264β = 90.00
c = 251.484γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
DENZOdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references