› 6bxk

X-ray diffraction
2.35Å resolution

Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and MTA

Released:
DOI: 10.2210/pdb6bxk/pdb
PDB entry 6bxk coloured by chain, front view.
PDB entry 6bxk coloured by chain, side view.
PDB entry 6bxk coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
Dong M, Kathiresan V, Fenwick MK, Torelli AT, Zhang Y, Caranto JD, Dzikovski B, Sharma A, Lancaster KM, Freed JH, Ealick SE, Hoffman BM, Lin H
Science 359 1247-1250 (2018)
PMID: 29590073

Function and Biology Details

Reaction catalysed: 
L-histidine-[translation elongation factor 2] + S-adenosyl-L-methionine = 2-((3S)-3-amino-3-carboxypropyl)-L-histidine-[translation elongation factor 2] + S-methyl-5'-thioadenosine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129773 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-(3-amino-3-carboxypropyl)histidine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 378 amino acids
Theoretical weight: 42.54 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O58832 (Residues: 1-342; Coverage: 100%)
Gene names: PH1105, dph2
Sequence domains: Putative diphthamide synthesis protein
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MTA 2 x MTA
Ligand SO4 2 x SO4
Ligand SF4 2 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 55.509Å b: 80.458Å c: 161.92Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.18 0.25
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer.
Hawer et al. (2018)
3 more

1 mention without citation

Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.
Dong et al. (2018)