› 6fd5

X-ray diffraction
1.55Å resolution

Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 14 days post crystallization (with AMP and PPi products partially generated)

Released:
DOI: 10.2210/pdb6fd5/pdb
PDB entry 6fd5 coloured by chain, front view.
PDB entry 6fd5 coloured by chain, side view.
PDB entry 6fd5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase.
Huyet J, Ozeir M, Burgevin MC, Pinson B, Chesney F, Remy JM, Siddiqi AR, Lupoli R, Pinon G, Saint-Marc C, Gibert JF, Morales R, Ceballos-Picot I, Barouki R, Daignan-Fornier B, Olivier-Bandini A, Augé F, Nioche P
Cell Chem Biol 25 666-676.e4 (2018)
PMID: 29576532

Function and Biology Details

Reaction catalysed: 
AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139738 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Adenine phosphoribosyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 178 amino acids
Theoretical weight: 19.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07741 (Residues: 3-180; Coverage: 99%)
Gene name: APRT
Sequence domains: Phosphoribosyl transferase domain
Structure domains: Rossmann fold

Ligands and Environments

5 bound ligands:
Ligand AMP 2 x AMP
Ligand PPV 2 x PPV
Ligand MG 2 x MG
Ligand GOL 1 x GOL
Ligand PRP 1 x PRP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P1
Unit cell:
a: 47.232Å b: 47.75Å c: 48.039Å
α: 77.3° β: 61.71° γ: 69.47°
R-values:
R R work R free
0.176 0.175 0.201
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Yeast to Study Human Purine Metabolism Diseases.
Daignan-Fornier et al. (2019)
2 more

1 mention without citation

Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction.
Ozeir et al. (2019)