4MU1

The structure of wt A. thaliana IGPD2 in complex with Mn2+, imidazole, and sulfate at 1.5 A resolution

Summary for 4MU1

• Entry DOI: 10.2210/pdb4mu1/pdb
• Related: 4MU0 4MU2 4MU3 4MU4
• Descriptor: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic, MANGANESE (II) ION, IMIDAZOLE, ... (6 entities in total)
• Functional Keywords: hydro-lyase, histidine biosynthesis, manganese binding, chloroplastic, lyase
• Biological source: Arabidopsis thaliana (mouse-ear cress)
• Cellular location: Plastid, chloroplast : O23346
• Total number of polymer chains: 1
• Total formula weight: 24240.75

Authors

Bisson, C.,Britton, K.L.,Sedelnikova, S.E.,Baker, P.J.,Rice, D.W. (deposition date: 2013-09-20, release date: 2014-09-24, Last modification date: 2023-09-20)

Primary citation

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.
Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination.
Structure, 23:1236-1245, 2015

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.

PubMed: 26095028
DOI: 10.1016/j.str.2015.05.012

Experimental method

X-RAY DIFFRACTION (1.5 Å)