› 5vcm

X-ray diffraction
1.6Å resolution

Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase with bound UDP and Manganese

Released:
DOI: 10.2210/pdb5vcm/pdb
PDB entry 5vcm coloured by chain, front view.
PDB entry 5vcm coloured by chain, side view.
PDB entry 5vcm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human N-acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite.
Kadirvelraj R, Yang JY, Sanders JH, Liu L, Ramiah A, Prabhakar PK, Boons GJ, Wood ZA, Moremen KW
Proc Natl Acad Sci U S A 115 4637-4642 (2018)
PMID: 29666272

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-alpha-D-glucosamine + beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-(alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc-N-Asn-[protein] = UDP + beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->3)-(beta-D-GlcNAc-(1->2)-alpha-D-Man-(1->6))-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc-N-Asn-[protein]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171223 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 419 amino acids
Theoretical weight: 48.35 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q10469 (Residues: 29-447; Coverage: 94%)
Gene name: MGAT2
Sequence domains: N-acetylglucosaminyltransferase II (MGAT2)

Ligands and Environments

5 bound ligands:
Ligand MN 2 x MN
Ligand UDP 1 x UDP
Ligand DMS 8 x DMS
Ligand EDO 1 x EDO
Ligand NAG 1 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 46.13Å b: 139.33Å c: 63.21Å
α: 90° β: 111.08° γ: 90°
R-values:
R R work R free
0.187 0.186 0.22
Expression system: Homo sapiens

Quick links

Citations

4 review citations

Promiscuity and specificity of eukaryotic glycosyltransferases.
Biswas et al. (2020)
3 more

5 mentions without citation

3D Structure and Function of Glycosyltransferases Involved in N-glycan Maturation.
Nagae et al. (2020)
4 more