Biological Assembly 1  

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

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content

• Total Structure Weight: 23.29 kDa 
• Atom Count: 1753 
• Modelled Residue Count: 186 
• Deposited Residue Count: 205 
• Unique protein chains: 1

4MU3

The form A structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and a mixture of its substrate, 2R3S-IGP, and an inhibitor, 2S3S-IGP, to 1.12 A resolution

• PDB DOI: 10.2210/pdb4MU3/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-09-20 Released: 2014-09-24 
• Deposition Author(s): Bisson, C., Britton, K.L., Sedelnikova, S.E., Baker, P.J., Rice, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.139 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 

Literature

Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination.

Bisson, C., Britton, K.L., Sedelnikova, S.E., Rodgers, H.F., Eadsforth, T.C., Viner, R.C., Hawkes, T.R., Baker, P.J., Rice, D.W.

(2015) Structure 23: 1236-1245

• PubMed: 26095028 
• DOI: 10.1016/j.str.2015.05.012
• Primary Citation of Related Structures:  
  4MU0, 4MU1, 4MU3, 4MU4, 4QNJ, 4QNK


• PubMed Abstract: 
  

Imidazoleglycerol-phosphate dehydratase (IGPD) catalyzes the Mn(II)-dependent dehydration of imidazoleglycerol phosphate (IGP) to 3-(1H-imidazol-4-yl)-2-oxopropyl dihydrogen phosphate during biosynthesis of histidine. As part of a program of herbicide design, we have determined a series of high-resolution crystal structures of an inactive mutant of IGPD2 from Arabidopsis thaliana in complex with IGP. The structures represent snapshots of the enzyme trapped at different stages of the catalytic cycle and show how substrate binding triggers a switch in the coordination state of an active site Mn(II) between six- and five-coordinate species. This switch is critical to prime the active site for catalysis, by facilitating the formation of a high-energy imidazolate intermediate. This work not only provides evidence for the molecular processes that dominate catalysis in IGPD, but also describes how the manipulation of metal coordination can be linked to discrete steps in catalysis, demonstrating one way that metalloenzymes exploit the unique properties of metal ions to diversify their chemistry.

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Organizational Affiliation: 

Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imidazoleglycerol-phosphate dehydratase 2, chloroplastic	A	205	Arabidopsis thaliana	Mutation(s): 1  Gene Names: At4g14910, dl3495c, HISN5B EC: 4.2.1.19
UniProt
Find proteins for O23346 (Arabidopsis thaliana) Explore O23346  Go to UniProtKB:  O23346

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IYP	E [auth A]	(2R,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate C6 H11 N2 O6 P HFYBTHCYPKEDQQ-RITPCOANSA-N
IG2	D [auth A]	(2S,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate C6 H11 N2 O6 P HFYBTHCYPKEDQQ-WDSKDSINSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.139 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 
• Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.1	α = 90
b = 113.1	β = 90
c = 113.1	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-20 
• Released Date: 2014-09-24 
Deposition Author(s): Bisson, C., Britton, K.L., Sedelnikova, S.E., Baker, P.J., Rice, D.W.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2015-07-22
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description