4D0T | pdb_00004d0t

GalNAc-T2 crystal soaked with UDP-GalNAc, EA2 peptide and manganese

• PDB DOI: https://doi.org/10.2210/pdb4D0T/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2014-04-30 Released: 2014-05-28 
• Deposition Author(s): 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.241 (Depositor) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

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

• PubMed: 24954443 
• DOI: https://doi.org/10.1002/anie.201402781
• Primary Citation 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. 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).

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 395.14 kDa 
• Atom Count: 24,500 
• Modeled Residue Count: 2,976 
• Deposited Residue Count: 3,442 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2	A, B, C, D, E, F	571	Homo sapiens	Mutation(s): 1  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 GTEx:  ENSG00000143641

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE	G [auth P], H [auth Z]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD2	DA [auth F], L [auth A], P [auth B], V [auth D], Z [auth E]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-NESSUJCYSA-N
UDP	R [auth C]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NGA	EA [auth P]	2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N
EDO	AA [auth E], BA [auth E], J [auth A], K [auth A], N [auth B], O [auth B], S [auth C], T [auth C], W [auth D], X [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	CA [auth F], I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.241 (Depositor) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.217	α = 90
b = 122.372	β = 90
c = 249.724	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-28 
Deposition Author(s): 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.

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, Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Structure summary