› 8k05

X-ray diffraction
1.45Å resolution

Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- sulfate bound holoenzyme

Released:
DOI: 10.2210/pdb8k05/pdb
PDB entry 8k05 coloured by chain, front view.
PDB entry 8k05 coloured by chain, side view.
PDB entry 8k05 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana.
Lee J, Kim SH, Rhee S
OpenAccess logo RNA Biol 21 1-10 (2024)
PMID: 38117089

Function and Biology Details

Reaction catalysed: 
Uracil + D-ribose 5-phosphate = pseudouridine 5'-phosphate + H(2)O
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-244449 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pseudouridine-5'-phosphate glycosidase Chain: A
Molecule details ›
Chain: A
Length: 340 amino acids
Theoretical weight: 36.18 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q84K35 (Residues: 1-330; Coverage: 100%)
Gene names: At1g50510, F11F12.14, PUMY
Sequence domains: Indigoidine synthase A like protein

Ligands and Environments

2 bound ligands:
Ligand MN 1 x MN
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 7A (6B, 6C1)
Spacegroup: P213
Unit cell:
a: 121.126Å b: 121.126Å c: 121.126Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.206 0.217
Expression system: Escherichia coli

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