› 1j93

X-ray diffraction
2.3Å resolution

Crystal Structure and Substrate Binding Modeling of the Uroporphyrinogen-III Decarboxylase from Nicotiana tabacum: Implications for the Catalytic Mechanism

Released:
DOI: 10.2210/pdb1j93/pdb
PDB entry 1j93 coloured by chain, front view.
PDB entry 1j93 coloured by chain, side view.
PDB entry 1j93 coloured by chain, top view.
Source organism: Nicotiana tabacum
Primary publication:
Crystal structure and substrate binding modeling of the uroporphyrinogen-III decarboxylase from Nicotiana tabacum. Implications for the catalytic mechanism.
Martins BM, Grimm B, Mock HP, Huber R, Messerschmidt A
J Biol Chem 276 44108-16 (2001)
PMID: 11524417

Function and Biology Details

Reaction catalysed: 
Uroporphyrinogen III = coproporphyrinogen + 4 CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-174978 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uroporphyrinogen decarboxylase, chloroplastic Chain: A
Molecule details ›
Chain: A
Length: 353 amino acids
Theoretical weight: 39.19 KDa
Source organism: Nicotiana tabacum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q42967 (Residues: 39-391; Coverage: 90%)
Gene name: DCUP
Sequence domains: Uroporphyrinogen decarboxylase (URO-D)
Structure domains: TIM Barrel

Ligands and Environments

1 bound ligand:
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MPG/DESY, HAMBURG BEAMLINE BW6
Spacegroup: P622
Unit cell:
a: 158.44Å b: 158.44Å c: 67.68Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.209 0.209 0.256
Expression system: Escherichia coli

Quick links

Citations

5 review citations

The biochemistry of heme biosynthesis.
Heinemann et al. (2008)
4 more

1 mention without citation

Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase.
Phillips et al. (2003)