› 6wug

X-ray diffraction
1.9Å resolution

Crystal Structure of S. pombe Rai1 in complex with 3'-FADP

Released:
DOI: 10.2210/pdb6wug/pdb
PDB entry 6wug coloured by chain, front view.
PDB entry 6wug coloured by chain, side view.
PDB entry 6wug coloured by chain, top view.
Source organism: Schizosaccharomyces pombe
Primary publication:
DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs.
Doamekpor SK, Grudzien-Nogalska E, Mlynarska-Cieslak A, Kowalska J, Kiledjian M, Tong L
OpenAccess logo Nucleic Acids Res 48 6136-6148 (2020)
PMID: 32374864

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-517961 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Decapping nuclease din1 Chain: A
Molecule details ›
Chain: A
Length: 372 amino acids
Theoretical weight: 42.97 KDa
Source organism: Schizosaccharomyces pombe
Expression system: Escherichia coli
UniProt:
  • Canonical: O13836 (Residues: 1-352; Coverage: 100%)
Gene names: SPAC19D5.06c, din1, rai1
Sequence domains: RAI1 like PD-(D/E)XK nuclease

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand UBG 1 x UBG
Ligand EDO 1 x EDO
1 modified residue:
Ligand CSS 1 x CSS

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2
Unit cell:
a: 100.594Å b: 59.978Å c: 72.545Å
α: 90° β: 104.67° γ: 90°
R-values:
R R work R free
0.193 0.191 0.229
Expression system: Escherichia coli

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Citations

6 review citations

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