› 3h0v

X-ray diffraction
2.24Å resolution

Human AdoMetDC with 5'-Deoxy-5'-(dimethylsulfonio) adenosine

Released:
DOI: 10.2210/pdb3h0v/pdb
PDB entry 3h0v coloured by chain, front view.
PDB entry 3h0v coloured by chain, side view.
PDB entry 3h0v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Role of the sulfonium center in determining the ligand specificity of human s-adenosylmethionine decarboxylase.
Bale S, Brooks W, Hanes JW, Mahesan AM, Guida WC, Ealick SE
Biochemistry 48 6423-30 (2009)
PMID: 19527050

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine = S-adenosyl 3-(methylthio)propylamine + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148140 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
S-adenosylmethionine decarboxylase beta chain Chain: B
Molecule details ›
Chain: B
Length: 67 amino acids
Theoretical weight: 7.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17707 (Residues: 1-67; Coverage: 20%)
Gene names: AMD, AMD1
Structure domains: S-adenosylmethionine decarboxylase
S-adenosylmethionine decarboxylase alpha chain Chain: A
Molecule details ›
Chain: A
Length: 266 amino acids
Theoretical weight: 30.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P17707 (Residues: 69-334; Coverage: 80%)
Gene names: AMD, AMD1
Sequence domains: Adenosylmethionine decarboxylase
Structure domains: S-adenosylmethionine decarboxylase

Ligands and Environments

3 bound ligands:
Ligand PUT 1 x PUT
Ligand M2T 1 x M2T
Ligand PYR 1 x PYR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 8-BM
Spacegroup: C2
Unit cell:
a: 93.852Å b: 49.535Å c: 69.998Å
α: 90° β: 105.03° γ: 90°
R-values:
R R work R free
0.227 0.227 0.275
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structural biology of S-adenosylmethionine decarboxylase.
Bale et al. (2010)
5 other articles

2 mentions without citation

Discovery of novel inhibitors of human S-adenosylmethionine decarboxylase based on in silico high-throughput screening and a non-radioactive enzymatic assay.
Liao et al. (2015)
1 more