› 6xxk

X-ray diffraction
1.65Å resolution

Crystal Structure of Human Deoxyhypusine Synthase in complex with spermidine

Released:
DOI: 10.2210/pdb6xxk/pdb
PDB entry 6xxk coloured by chain, front view.
PDB entry 6xxk coloured by chain, side view.
PDB entry 6xxk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase.
Wątor E, Wilk P, Grudnik P
Biomolecules 10 (2020)
PMID: 32235505

Function and Biology Details

Reaction catalysed: 
(1a) spermidine + NAD(+) = dehydrospermidine + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155939 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyhypusine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 369 amino acids
Theoretical weight: 41.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49366 (Residues: 1-369; Coverage: 100%)
Gene names: DHPS, DS
Sequence domains: Deoxyhypusine synthase

Ligands and Environments

6 bound ligands:
Ligand SPD 2 x SPD
Ligand EDO 14 x EDO
Ligand ACT 9 x ACT
Ligand BME 4 x BME
Ligand FMT 11 x FMT
Ligand MRD 1 x MRD
1 modified residue:
Ligand CSS 2 x CSS

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P3221
Unit cell:
a: 104.98Å b: 104.98Å c: 160.898Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.155 0.155 0.162
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Hypusination, a Metabolic Posttranslational Modification of eIF5A in Plants during Development and Environmental Stress Responses.
Pálfi et al. (2021)
9 other articles

3 mentions without citation

Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase.
Wątor et al. (2020)
2 more