› 6vtd

X-ray diffraction
2.4Å resolution

Naegleria gruberi RNA ligase R149A mutant with ATP and Mn

Released:
DOI: 10.2210/pdb6vtd/pdb
PDB entry 6vtd coloured by chain, front view.
PDB entry 6vtd coloured by chain, side view.
PDB entry 6vtd coloured by chain, top view.
Source organism: Naegleria gruberi
Primary publication:
Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Unciuleac MC, Goldgur Y, Shuman S
OpenAccess logo Nucleic Acids Res 48 5603-5615 (2020)
PMID: 32315072

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112420 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA ligase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 340 amino acids
Theoretical weight: 38.58 KDa
Source organism: Naegleria gruberi
Expression system: Escherichia coli
UniProt:
  • Canonical: D2W2Z5 (Residues: 1-339; Coverage: 100%)
Gene name: NAEGRDRAFT_82186
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand MN 3 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P41212
Unit cell:
a: 88.775Å b: 88.775Å c: 100.926Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.252 0.246 0.306
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Classification of domains in predicted structures of the human proteome.
Schaeffer et al. (2023)

1 mention without citation

Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Unciuleac et al. (2020)