Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.43 kDa 
• Atom Count: 2963 
• Modelled Residue Count: 329 
• Deposited Residue Count: 337 
• Unique protein chains: 1

2WOQ

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

• PDB DOI: 10.2210/pdb2WOQ/pdb

• Classification: LYASE/ANTIBIOTIC
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-07-27 Released: 2009-10-27 
• Deposition Author(s): Heinemann, I.U., Schulz, C., Schubert, W.-D., Heinz, D.W., Wang, Y.-G., Kobayashi, Y., Awa, Y., Wachi, M., Jahn, D., Jahn, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.180 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 

Literature

Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin.

Heinemann, I.U., Schulz, C., Schubert, W.D., Heinz, D.W., Wang, Y.G., Kobayashi, Y., Awa, Y., Wachi, M., Jahn, D., Jahn, M.

(2010) Antimicrob Agents Chemother 54: 267-272

• PubMed: 19822707 
• DOI: 10.1128/AAC.00553-09
• Primary Citation of Related Structures:  
  2WOQ


• PubMed Abstract: 
  

The recently discovered antibacterial compound alaremycin, produced by Streptomyces sp. A012304, structurally closely resembles 5-aminolevulinic acid, the substrate of porphobilinogen synthase. During the initial steps of heme biosynthesis, two molecules of 5-aminolevulinic acid are asymmetrically condensed to porphobilinogen. Alaremycin was found to efficiently inhibit the growth of both Gram-negative and Gram-positive bacteria. Using the newly created heme-permeable strain Escherichia coli CSA1, we are able to uncouple heme biosynthesis from bacterial growth and demonstrate that alaremycin targets the heme biosynthetic pathway. Further studies focused on the activity of alaremycin against the opportunistic pathogenic bacterium Pseudomonas aeruginosa. The MIC of alaremycin was determined to be 12 mM. Alaremycin was identified as a direct inhibitor of recombinant purified P. aeruginosa porphobilinogen synthase and had a K(i) of 1.33 mM. To understand the molecular basis of alaremycin's antibiotic activity at the atomic level, the P. aeruginosa porphobilinogen synthase was cocrystallized with the alaremycin. At 1.75-A resolution, the crystal structure reveals that the antibiotic efficiently blocks the active site of porphobilinogen synthase. The antibiotic binds as a reduced derivative of 5-acetamido-4-oxo-5-hexenoic acid. The corresponding methyl group is, however, not coordinated by any amino acid residues of the active site, excluding its functional relevance for alaremycin inhibition. Alaremycin is covalently bound by the catalytically important active-site lysine residue 260 and is tightly coordinated by several active-site amino acids. Our data provide a solid structural basis to further improve the activity of alaremycin for rational drug design. Potential approaches are discussed.

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Organizational Affiliation: 

Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, Braunschweig D-38106, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA-AMINOLEVULINIC ACID DEHYDRATASE	A	337	Pseudomonas aeruginosa	Mutation(s): 0  EC: 4.2.1.24
UniProt
Find proteins for Q59643 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q59643  Go to UniProtKB:  Q59643

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE5	I [auth A], J [auth A], K [auth A], L [auth A]	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
EPE	G [auth A], H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
AYC	B [auth A]	ALAREMYCIN 2 C8 H13 N O4 QSRUAKBTZTXXLM-RXMQYKEDSA-N
MG	C [auth A], D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AYC	PDBBind:  2WOQ	Ki: 1.33e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.180 
• R-Value Work: 0.146 
• R-Value Observed: 0.147 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.444	α = 90
b = 84.444	β = 90
c = 158.528	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-27 
• Released Date: 2009-10-27 
Deposition Author(s): Heinemann, I.U., Schulz, C., Schubert, W.-D., Heinz, D.W., Wang, Y.-G., Kobayashi, Y., Awa, Y., Wachi, M., Jahn, D., Jahn, M.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references, Derived calculations, Experimental preparation, Other