› 6q2e

X-ray diffraction
1.77Å resolution

Crystal structure of Methanobrevibacter smithii Dph2 bound to 5'-methylthioadenosine

Released:
DOI: 10.2210/pdb6q2e/pdb
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PDB entry 6q2e coloured by chain, front view.
PDB entry 6q2e coloured by chain, side view.
PDB entry 6q2e coloured by chain, top view.
Source organism: Methanobrevibacter smithii
Primary publication:
The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.
Fenwick MK, Dong M, Lin H, Ealick SE
Biochemistry 58 4343-4351 (2019)
PMID: 31566354

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-107754 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-(3-amino-3-carboxypropyl)histidine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 337 amino acids
Theoretical weight: 38.43 KDa
Source organism: Methanobrevibacter smithii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5UMY5 (Residues: 1-334; Coverage: 100%)
Gene name: Msm_1358
Sequence domains: Putative diphthamide synthesis protein

Ligands and Environments

3 bound ligands:
Ligand MTA 2 x MTA
Ligand SF4 2 x SF4
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 63.082Å b: 81.02Å c: 130.972Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.219
Expression system: Escherichia coli BL21(DE3)

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Citations

4 citation in other articles

Structural basis of elongation factor 2 switching.
Fenwick et al. (2020)
3 more

1 mention without citation

The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.
Fenwick et al. (2019)

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