4D0Z

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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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:  
    4D0T, 4D0Z, 4D11

  • 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 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2
A, B, C, D, E, F
A, B, C, D, E, F
571Homo sapiensMutation(s): 1 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10471
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDEG [auth X],
H [auth Y]		6Homo sapiensMutation(s): 0 
Gene Names: CYR61, hCG_23652
UniProt
Find proteins for Q6FI18 (Homo sapiens)
Explore Q6FI18 
Go to UniProtKB:  Q6FI18
Entity Groups  
UniProt GroupQ6FI18
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HWU
Query on HWU
Download Ideal Coordinates CCD File 
FB [auth E],
GA [auth C],
IB [auth F],
JA [auth D],
U [auth A],
FB [auth E],
GA [auth C],
IB [auth F],
JA [auth D],
U [auth A],
W [auth B]
(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
C17 H27 N3 O16 P2 S
JPRVHSQHWXZSNC-KZEZZKTRSA-N		 Ligand Interaction
BBK
Query on BBK
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EB [auth E],
FA [auth B],
KA [auth D],
T [auth A]		2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose
C8 H15 N O5 S
DYCCLPFFILCZGU-CBQIKETKSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth B],
AB [auth E],
BA [auth B],
BB [auth E],
CA [auth B],
AA [auth B],
AB [auth E],
BA [auth B],
BB [auth E],
CA [auth B],
CB [auth E],
DA [auth B],
DB [auth E],
EA [auth B],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth E],
R [auth A],
RA [auth E],
S [auth A],
SA [auth E],
TA [auth E],
UA [auth E],
VA [auth E],
WA [auth E],
X [auth B],
XA [auth E],
Y [auth B],
YA [auth E],
Z [auth B],
ZA [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
MN
Query on MN
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GB [auth E],
HA [auth C],
HB [auth F],
I [auth A],
IA [auth D],
GB [auth E],
HA [auth C],
HB [auth F],
I [auth A],
IA [auth D],
V [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.485α = 90
b = 121.143β = 90
c = 249.387γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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