› 2woq

X-ray diffraction
1.75Å resolution

Porphobilinogen Synthase (HemB) in Complex with 5-acetamido-4- oxohexanoic acid (Alaremycin 2)

Released:
DOI: 10.2210/pdb2woq/pdb
PDB entry 2woq coloured by chain, front view.
PDB entry 2woq coloured by chain, side view.
PDB entry 2woq coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin.
Heinemann IU, Schulz C, Schubert WD, Heinz DW, Wang YG, Kobayashi Y, Awa Y, Wachi M, Jahn D, Jahn M
Antimicrob Agents Chemother 54 267-72 (2010)
PMID: 19822707

Function and Biology Details

Reaction catalysed: 
2 5-aminolevulinate = porphobilinogen + 2 H(2)O
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176810 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Delta-aminolevulinic acid dehydratase Chain: A
Molecule details ›
Chain: A
Length: 337 amino acids
Theoretical weight: 37.08 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q59643 (Residues: 1-337; Coverage: 100%)
Gene names: PA5243, hemB
Sequence domains: Delta-aminolevulinic acid dehydratase
Structure domains: Aldolase class I

Ligands and Environments

4 bound ligands:
Ligand AYC 1 x AYC
Ligand MG 4 x MG
Ligand EPE 2 x EPE
Ligand PE5 4 x PE5
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: I422
Unit cell:
a: 84.444Å b: 84.444Å c: 158.528Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.147 0.146 0.18
Expression system: Escherichia coli BL21

Quick links

Citations

1 review citation

Structure and function of enzymes in heme biosynthesis.
Layer et al. (2010)
7 other articles

2 mentions without citation

Crystal structure of Toxoplasma gondii porphobilinogen synthase: insights on octameric structure and porphobilinogen formation.
Jaffe et al. (2011)
1 more