› 4d0z

X-ray diffraction
2.2Å resolution

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

Released:
DOI: 10.2210/pdb4d0z/pdb
PDB entry 4d0z coloured by chain, front view.
PDB entry 4d0z coloured by chain, side view.
PDB entry 4d0z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substrate-guided front-face reaction revealed by combined structural snapshots and metadynamics for the polypeptide N-acetylgalactosaminyltransferase 2.
Lira-Navarrete E, Iglesias-Fernández J, Zandberg WF, Compañón I, Kong Y, Corzana F, Pinto BM, Clausen H, Peregrina JM, Vocadlo DJ, Rovira C, Hurtado-Guerrero R
Angew Chem Int Ed Engl 53 8206-10 (2014)
PMID: 24954443

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-galactosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-alpha-D-galactosaminyl)-L-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-171229 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Polypeptide N-acetylgalactosaminyltransferase 2 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 571 amino acids
Theoretical weight: 64.82 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q10471 (Residues: 1-571; Coverage: 100%)
Gene name: GALNT2
Sequence domains:
Structure domains:
CCN family member 1 Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 6 amino acids
Theoretical weight: 549 Da
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q6FI18 (Residues: 24-29; Coverage: 1%)
Gene names: CYR61, hCG_23652

Ligands and Environments

4 bound ligands:
Ligand MN 6 x MN
Ligand EDO 37 x EDO
Ligand BBK 4 x BBK
Ligand HWU 6 x HWU
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P212121
Unit cell:
a: 116.485Å b: 121.143Å c: 249.387Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.234
Expression system: Komagataella pastoris

Quick links

Citations

8 review citations

The Biochemistry of O-GlcNAc Transferase: Which Functions Make It Essential in Mammalian Cells?
Levine et al. (2016)
7 more

6 mentions without citation

Dynamic interplay between catalytic and lectin domains of GalNAc-transferases modulates protein O-glycosylation.
Lira-Navarrete et al. (2015)
5 more