› 4i5w

X-ray diffraction
2.79Å resolution

Crystal structure of yeast Ap4A phosphorylase Apa2 in complex with AMP

Released:
DOI: 10.2210/pdb4i5w/pdb
PDB entry 4i5w coloured by chain, front view.
PDB entry 4i5w coloured by chain, side view.
PDB entry 4i5w coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structures of yeast Apa2 reveal catalytic insights into a canonical AP₄A phosphorylase of the histidine triad superfamily.
Hou WT, Li WZ, Chen Y, Jiang YL, Zhou CZ
J Mol Biol 425 2687-98 (2013)
PMID: 23628156

Function and Biology Details

Reactions catalysed: 
ADP + sulfate = phosphate + adenylyl sulfate
ADP + ATP = phosphate + P(1),P(4)-bis(5'-adenosyl) tetraphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149526 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 333 amino acids
Theoretical weight: 37.9 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P22108 (Residues: 1-325; Coverage: 100%)
Gene names: APA2, D9719.33, YDR530C
Sequence domains:
Structure domains: HIT family, subunit A

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand AMP 4 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 52.846Å b: 70.327Å c: 174.237Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.224 0.261
Expression system: Escherichia coli

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Citations

2 review citations

Re-evaluation of Diadenosine Tetraphosphate (Ap4A) From a Stress Metabolite to Bona Fide Secondary Messenger.
Ferguson et al. (2020)
1 more