› 7aaj

X-ray diffraction
1.8Å resolution

Human porphobilinogen deaminase in complex with cofactor

Released:
DOI: 10.2210/pdb7aaj/pdb
PDB entry 7aaj coloured by chain, front view.
PDB entry 7aaj coloured by chain, side view.
PDB entry 7aaj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Characterization of porphobilinogen deaminase mutants reveals that arginine-173 is crucial for polypyrrole elongation mechanism.
Bustad HJ, Kallio JP, Laitaoja M, Toska K, Kursula I, Martinez A, Jänis J
iScience 24 102152 (2021)
PMID: 33665570

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140114 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Porphobilinogen deaminase Chains: A, B
Molecule details ›
Chains: A, B
Length: 363 amino acids
Theoretical weight: 39.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P08397 (Residues: 1-361; Coverage: 100%)
Gene names: HMBS, PBGD, UPS
Sequence domains:

Ligands and Environments


Cofactor: Ligand DPM 2 x DPM
1 bound ligand:
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: P212121
Unit cell:
a: 81.163Å b: 84.608Å c: 108.913Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.249 0.294
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Combining X-rays, neutrons and electrons, and NMR, for precision and accuracy in structure-function studies.
Helliwell JR. (2021)
2 more

3 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)
2 more