› 5m6r

X-ray diffraction
2.73Å resolution

Human porphobilinogen deaminase in complex with reaction intermediate

Released:
DOI: 10.2210/pdb5m6r/pdb
PDB entry 5m6r coloured by chain, front view.
PDB entry 5m6r coloured by chain, side view.
PDB entry 5m6r 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: 389 amino acids
Theoretical weight: 42.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P08397 (Residues: 1-361; Coverage: 100%)
Gene names: HMBS, PBGD, UPS
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 7J8 2 x 7J8
Ligand PO4 3 x PO4
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21
Unit cell:
a: 68.91Å b: 81.2Å c: 79.69Å
α: 90° β: 93.01° γ: 90°
R-values:
R R work R free
0.2 0.197 0.246
Expression system: Escherichia coli

Quick links

Citations

7 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)
6 more

9 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)
8 more