› 1pda

X-ray diffraction
1.76Å resolution

STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE

Released:
DOI: 10.2210/pdb1pda/pdb
PDB entry 1pda coloured by chain, front view.
PDB entry 1pda coloured by chain, side view.
PDB entry 1pda coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structure of porphobilinogen deaminase reveals a flexible multidomain polymerase with a single catalytic site.
Louie GV, Brownlie PD, Lambert R, Cooper JB, Blundell TL, Wood SP, Warren MJ, Woodcock SC, Jordan PM
Nature 359 33-9 (1992)
PMID: 1522882

Function and Biology Details

Reaction catalysed: 
4 porphobilinogen + H(2)O = hydroxymethylbilane + 4 NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139322 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Porphobilinogen deaminase Chain: A
Molecule details ›
Chain: A
Length: 313 amino acids
Theoretical weight: 33.89 KDa
Source organism: Escherichia coli
Expression system: Not provided
UniProt:
  • Canonical: P06983 (Residues: 1-313; Coverage: 100%)
Gene names: JW5932, b3805, hemC, popE
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand DPM 1 x DPM
1 bound ligand:
Ligand ACY 1 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: P21212
Unit cell:
a: 88Å b: 75.9Å c: 50.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.188 not available
Expression system: Not provided

Quick links

Citations

26 review citations

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

23 mentions without citation

Acute Intermittent Porphyria: An Overview of Therapy Developments and Future Perspectives Focusing on Stabilisation of HMBS and Proteostasis Regulators.
Bustad et al. (2021)
22 more