› 3ecr

X-ray diffraction
2.18Å resolution

Structure of human porphobilinogen deaminase

Released:
DOI: 10.2210/pdb3ecr/pdb
PDB entry 3ecr coloured by chain, front view.
PDB entry 3ecr coloured by chain, side view.
PDB entry 3ecr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insight into acute intermittent porphyria.
Song G, Li Y, Cheng C, Zhao Y, Gao A, Zhang R, Joachimiak A, Shaw N, Liu ZJ
FASEB J 23 396-404 (2009)
PMID: 18936296

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: 364 amino acids
Theoretical weight: 39.66 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


Cofactor: Ligand DPM 2 x DPM
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 71.61Å b: 81.061Å c: 109.211Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.232 0.271
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Structure and function of enzymes in heme biosynthesis.
Layer et al. (2010)
2 more

20 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)
19 more