› 5m7f

X-ray diffraction
2.78Å resolution

Human porphobilinogen deaminase in complex with DPM cofactor

Released:
DOI: 10.2210/pdb5m7f/pdb
PDB entry 5m7f coloured by chain, front view.
PDB entry 5m7f coloured by chain, side view.
PDB entry 5m7f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of pyrrole polymerization in human porphobilinogen deaminase.
Pluta P, Roversi P, Bernardo-Seisdedos G, Rojas AL, Cooper JB, Gu S, Pickersgill RW, Millet O
Biochim Biophys Acta Gen Subj 1862 1948-1955 (2018)
PMID: 29908816

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: 365 amino acids
Theoretical weight: 40.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P08397 (Residues: 18-361; Coverage: 95%)
Gene names: HMBS, PBGD, UPS
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand DPM 2 x DPM
1 bound ligand:
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21
Unit cell:
a: 70.42Å b: 80.95Å c: 76.22Å
α: 90° β: 95.7° γ: 90°
R-values:
R R work R free
0.222 0.22 0.26
Expression system: Escherichia coli

Quick links

Citations

10 citation in other articles

Crystal structures of hydroxymethylbilane synthase complexed with a substrate analog: a single substrate-binding site for four consecutive condensation steps.
Sato et al. (2021)
9 more

5 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)
4 more