3OBK

Crystal structure of delta-aminolevulinic acid dehydratase (porphobilinogen synthase) from toxoplasma gondii ME49 in complex with the reaction product porphobilinogen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Toxoplasma gondii Porphobilinogen Synthase: INSIGHTS ON OCTAMERIC STRUCTURE AND PORPHOBILINOGEN FORMATION.

Jaffe, E.K.Shanmugam, D.Gardberg, A.Dieterich, S.Sankaran, B.Stewart, L.J.Myler, P.J.Roos, D.S.

(2011) J Biol Chem 286: 15298-15307

  • DOI: https://doi.org/10.1074/jbc.M111.226225
  • Primary Citation of Related Structures:  
    3OBK

  • PubMed Abstract: 

    Porphobilinogen synthase (PBGS) is essential for heme biosynthesis, but the enzyme of the protozoan parasite Toxoplasma gondii (TgPBGS) differs from that of its human host in several important respects, including subcellular localization, metal ion dependence, and quaternary structural dynamics. We have solved the crystal structure of TgPBGS, which contains an octamer in the crystallographic asymmetric unit. Crystallized in the presence of substrate, each active site contains one molecule of the product porphobilinogen. Unlike prior structures containing a substrate-derived heterocycle directly bound to an active site zinc ion, the product-bound TgPBGS active site contains neither zinc nor magnesium, placing in question the common notion that all PBGS enzymes require an active site metal ion. Unlike human PBGS, the TgPBGS octamer contains magnesium ions at the intersections between pro-octamer dimers, which are presumed to function in allosteric regulation. TgPBGS includes N- and C-terminal regions that differ considerably from previously solved crystal structures. In particular, the C-terminal extension found in all apicomplexan PBGS enzymes forms an intersubunit β-sheet, stabilizing a pro-octamer dimer and preventing formation of hexamers that can form in human PBGS. The TgPBGS structure suggests strategies for the development of parasite-selective PBGS inhibitors.


  • Organizational Affiliation

    Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA. eileen.jaffe@fccc.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Delta-aminolevulinic acid dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H
356Toxoplasma gondii ME49Mutation(s): 0 
Gene Names: TGME49_053900
EC: 4.2.1.24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PBG
Query on PBG

Download Ideal Coordinates CCD File 
EA [auth D]
EB [auth H]
KA [auth E]
L [auth A]
QA [auth F]
EA [auth D],
EB [auth H],
KA [auth E],
L [auth A],
QA [auth F],
S [auth B],
YA [auth G],
Z [auth C]
3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID
C10 H14 N2 O4
QSHWIQZFGQKFMA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
AB [auth G]
BB [auth G]
FA [auth D]
FB [auth H]
AA [auth C],
AB [auth G],
BB [auth G],
FA [auth D],
FB [auth H],
GA [auth D],
GB [auth H],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
O [auth A],
RA [auth F],
SA [auth F],
T [auth B],
TA [auth F],
U [auth B],
Y [auth C],
ZA [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth D]
CB [auth H]
DA [auth D]
HA [auth E]
IA [auth E]
CA [auth D],
CB [auth H],
DA [auth D],
HA [auth E],
IA [auth E],
J [auth A],
K [auth A],
OA [auth F],
PA [auth F],
Q [auth B],
R [auth B],
UA [auth G],
V [auth C],
VA [auth G],
W [auth C],
XA [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
DB [auth H]
I [auth A]
JA [auth E]
NA [auth F]
BA [auth D],
DB [auth H],
I [auth A],
JA [auth E],
NA [auth F],
P [auth B],
WA [auth G],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.11α = 90
b = 187.17β = 90
c = 95.86γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description