4D11

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  
    4D0Z, 4D11, 4D0T

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLYPEPTIDE GALNAC-TRANSFERASE T2A, B, D, E, F571Homo sapiensMutation(s): 1 
Gene Names: GALNT2
EC: 2.4.1.41
Find proteins for Q10471 (Homo sapiens)
Explore Q10471 
Go to UniProtKB:  Q10471
NIH Common Fund Data Resources
PHAROS  Q10471
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POLYPEPTIDE GALNAC-TRANSFERASE T2C571Homo sapiensMutation(s): 1 
Gene Names: GALNT2
EC: 2.4.1.41
Find proteins for Q10471 (Homo sapiens)
Explore Q10471 
Go to UniProtKB:  Q10471
NIH Common Fund Data Resources
PHAROS  Q10471
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDEL, O, P, X, Z6Homo sapiensMutation(s): 0 
Gene Names: CYR61hCG_23652
Find proteins for Q6FI18 (Homo sapiens)
Explore Q6FI18 
Go to UniProtKB:  Q6FI18
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download CCD File 
A, B, C, D, E, F
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
BBK
Query on BBK

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

Download CCD File 
A, B, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.771α = 90
b = 120.898β = 90
c = 249.607γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2014-08-13
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Derived calculations, Other, Structure summary