Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 72.3 kDa 
• Atom Count: 5,419 
• Modelled Residue Count: 646 
• Deposited Residue Count: 646 
• Unique protein chains: 1

 1L6Y

Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid

• PDB DOI:  https://doi.org/10.2210/pdb1L6Y/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-03-14 Released: 2002-04-17 
• Deposition Author(s): Jaffe, E.K., Kervinen, J., Martins, J., Stauffer, F., Neier, R., Wlodawer, A., Zdanov, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.206 

Literature

Species-Specific Inhibition of Porphobilinogen Synthase by 4-Oxosebacic Acid

Jaffe, E.K., Kervinen, J., Martins, J., Stauffer, F., Neier, R., Wlodawer, A., Zdanov, A.

(2002) J Biol Chem 277: 19792-19799

• PubMed: 11909869 
• DOI: https://doi.org/10.1074/jbc.M201486200
• Primary Citation of Related Structures:  
  1L6S, 1L6Y


• PubMed Abstract: 
  

Porphobilinogen synthase (PBGS) catalyzes the condensation of two molecules of 5-aminolevulinic acid (ALA), an essential step in tetrapyrrole biosynthesis. 4-Oxosebacic acid (4-OSA) and 4,7-dioxosebacic acid (4,7-DOSA) are bisubstrate reaction intermediate analogs for PBGS. We show that 4-OSA is an active site-directed irreversible inhibitor for Escherichia coli PBGS, whereas human, pea, Pseudomonas aeruginosa, and Bradyrhizobium japonicum PBGS are insensitive to inhibition by 4-OSA. Some variants of human PBGS (engineered to resemble E. coli PBGS) have increased sensitivity to inactivation by 4-OSA, suggesting a structural basis for the specificity. The specificity of 4-OSA as a PBGS inhibitor is significantly narrower than that of 4,7-DOSA. Comparison of the crystal structures for E. coli PBGS inactivated by 4-OSA versus 4,7-DOSA shows significant variation in the half of the inhibitor that mimics the second substrate molecule (A-side ALA). Compensatory changes occur in the structure of the active site lid, which suggests that similar changes normally occur to accommodate numerous hybridization changes that must occur at C3 of A-side ALA during the PBGS-catalyzed reaction. A comparison of these with other PBGS structures identifies highly conserved active site water molecules, which are isolated from bulk solvent and implicated as proton acceptors in the PBGS-catalyzed reaction.

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Related Citations: 

• Mechanistic Basis for Suicide Inactivation of Porphobilinogen Synthase by 4,7-dioxosebacic acid, an Inhibitor that Shows Dramatic Species Selectivity
  Kervinen, J., Jaffe, E.K., Stauffer, F., Neier, R., Wlodawer, A., Zdanov, A.
  (2001) Biochemistry 40: 8227

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Organizational Affiliation: 

Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PORPHOBILINOGEN SYNTHASE	A, B	323	Escherichia coli	Mutation(s): 1  EC: 4.2.1.24
UniProt
Find proteins for P0ACB2 (Escherichia coli (strain K12)) Explore P0ACB2  Go to UniProtKB:  P0ACB2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4OX	E [auth A], L [auth B]	4-OXODECANEDIOIC ACID C10 H16 O5 XTQIBFVBYWIHIP-UHFFFAOYSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
4OX	PDBBind:  1L6Y	IC50: 2.20e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.206 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129	α = 90
b = 129	β = 90
c = 142.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-17 
Deposition Author(s): Jaffe, E.K., Kervinen, J., Martins, J., Stauffer, F., Neier, R., Wlodawer, A., Zdanov, A.

Revision History  

• Version 1.0: 2002-04-17
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance