› 1wde

X-ray diffraction
2Å resolution

Crystal structure of the conserved hypothetical protein APE0931 from Aeropyrum pernix K1

Released:
DOI: 10.2210/pdb1wde/pdb
PDB entry 1wde coloured by chain, front view.
PDB entry 1wde coloured by chain, side view.
PDB entry 1wde coloured by chain, top view.
Source organism: Aeropyrum pernix
Primary publication:
Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2.
Kishishita S, Shimizu K, Murayama K, Terada T, Shirouzu M, Yokoyama S, Kunishima N
Acta Crystallogr D Biol Crystallogr 64 397-406 (2008)
PMID: 18391406

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + 2-((3S)-3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-((3S)-3-carboxy-3-(methylamino)propyl)-L-histidine-[translation elongation factor 2]
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-195474 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diphthine synthase Chain: A
Molecule details ›
Chain: A
Length: 294 amino acids
Theoretical weight: 31.76 KDa
Source organism: Aeropyrum pernix
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9YDI2 (Residues: 1-294; Coverage: 100%)
Gene names: APE_0931, dphB
Sequence domains: Tetrapyrrole (Corrin/Porphyrin) Methylases
Structure domains:

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P41212
Unit cell:
a: 62.827Å b: 62.827Å c: 129.728Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.199 0.244
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Methyltransferases: Functions and Applications.
Abdelraheem et al. (2022)
2 other articles

1 mention without citation

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations.
Ortiz et al. (1998)