4D0Z

GalNAc-T2 crystal soaked with UDP-5SGalNAc, mEA2 and manganese (Higher resolution dataset)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate-Guided Front-Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N- Acetylgalactosaminyltransferase 2.

Lira-Navarrete, E.Iglesias-Fernandez, J.Zandberg, W.F.Companon, I.Kong, Y.Corzana, F.Pinto, B.M.Clausen, H.Peregrina, J.M.Vocadlo, D.Rovira, C.Hurtado-Guerrero, R.

(2014) Angew.Chem.Int.Ed.Engl. 53: 8206

  • DOI: 10.1002/anie.201402781
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The retaining glycosyltransferase GalNAc-T2 is a member of a large family of human polypeptide GalNAc-transferases that is responsible for the post-translational modification of many cell-surface proteins. By the use of combined structural and comput ...

    The retaining glycosyltransferase GalNAc-T2 is a member of a large family of human polypeptide GalNAc-transferases that is responsible for the post-translational modification of many cell-surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum-mechanics/molecular-mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic-electronic level of detail. Our study provides a detailed structural rationale for an ordered bi-bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front-face SN i-type reaction in which the substrate N-acetyl sugar substituent coordinates efficient glycosyl transfer.


    Organizational Affiliation

    Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Fundacion ARAID, Edificio Pignatelli 36 (Spain).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2
A, B, C, D, E, F
571Homo sapiensMutation(s): 1 
Gene Names: GALNT2
EC: 2.4.1.41
Find proteins for Q10471 (Homo sapiens)
Go to Gene View: GALNT2
Go to UniProtKB:  Q10471
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE
X, Y
6Homo sapiensMutation(s): 0 
Gene Names: CYR61
Find proteins for Q6FI18 (Homo sapiens)
Go to Gene View: CYR61
Go to UniProtKB:  Q6FI18
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
HWU
Query on HWU

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
URIDINE DIPHOSPHO-5-THIO-N-ACETYLGALACTOSAMINE
C17 H27 N3 O16 P2 S
JPRVHSQHWXZSNC-KZEZZKTRSA-N
 Ligand Interaction
BBK
Query on BBK

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Download CCD File 
A, B, D, E
2-(acetylamino)-2-deoxy-5-thio-alpha-D-galactopyranose
C8 H15 N O5 S
DYCCLPFFILCZGU-CBQIKETKSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, D, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 116.485α = 90.00
b = 121.143β = 90.00
c = 249.387γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-07-02
    Type: Database references
  • Version 1.2: 2014-08-13
    Type: Database references