› 7nut

X-ray diffraction
1.9Å resolution

Crystal structure of human AMDHD2 in complex with Zn and GlcN6P

Released:
DOI: 10.2210/pdb7nut/pdb
PDB entry 7nut coloured by chain, front view.
PDB entry 7nut coloured by chain, side view.
PDB entry 7nut coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway.
Kroef V, Ruegenberg S, Horn M, Allmeroth K, Ebert L, Bozkus S, Miethe S, Elling U, Schermer B, Baumann U, Denzel MS
Elife 11 (2022)
PMID: 35229715

Function and Biology Details

Reaction catalysed: 
N-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195176 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-acetylglucosamine-6-phosphate deacetylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 409 amino acids
Theoretical weight: 43.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y303 (Residues: 1-409; Coverage: 100%)
Gene names: AMDHD2, CGI-14
Sequence domains: Amidohydrolase family

Ligands and Environments

2 bound ligands:
Ligand GLP 2 x GLP
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 63.261Å b: 161.449Å c: 86.621Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.185 0.213
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Integration of O-GlcNAc into Stress Response Pathways.
Fahie et al. (2022)
4 more

1 mention without citation

GFPT2/GFAT2 and AMDHD2 act in tandem to control the hexosamine pathway.
Kroef et al. (2022)