1IZC

Crystal Structure Analysis of Macrophomate synthase

Summary for 1IZC

• Entry DOI: 10.2210/pdb1izc/pdb
• Descriptor: macrophomate synthase intermolecular Diels-Alderase, MAGNESIUM ION, PYRUVIC ACID, ... (4 entities in total)
• Functional Keywords: tim-barrel, pyruvate mg(ii) complex, lyase
• Biological source: Macrophoma commelinae
• Total number of polymer chains: 1
• Total formula weight: 36384.26

Authors

Ose, T.,Watanabe, K.,Mie, T.,Honma, M.,Watanabe, H.,Yao, M.,Oikawa, H.,Tanaka, I. (deposition date: 2002-10-01, release date: 2003-04-01, Last modification date: 2025-08-06)

Primary citation

Ose, T.,Watanabe, K.,Yao, M.,Honma, M.,Oikawa, H.,Tanaka, I.
Structure of macrophomate synthase.
Acta Crystallogr.,Sect.D, 60:1187-1197, 2004

PubMed Abstract: Macrophomate synthase (MPS) is an enzyme that catalyzes an extraordinarily complex conversion reaction, including two decarboxylations, two carbon-carbon bond formations and a dehydration, to form the benzoate analogue macrophomate from a 2-pyrone derivative and oxalacetate. Of these reactions, the two carbon-carbon bond formations are especially noteworthy because previous experiments have indicated that they proceed via a Diels-Alder reaction, one of the most widely used reactions in organic synthesis. The structural evidence that MPS catalyzes an intermolecular Diels-Alder reaction has been reported recently [Ose et al. (2003), Nature (London), 422, 185-189]. Interestingly, the tertiary structure as well as the quaternary structure of MPS are similar to those of 2-dehydro-3-deoxygalactarate (DDG) aldolase, a carbon-carbon bond-forming enzyme that catalyzes the reversible reaction of aldol condensation/cleavage. Here, the structure of MPS is described in detail and compared with that of DDG aldolase. Both enzymes have a (beta/alpha)(8)-barrel fold and are classified as belonging to the enolase superfamily based on their reaction strategy. The basic principles for carbon-carbon bond formation used by both MPS and DDG aldolase are the same with regard to trapping the enolate substrate and inducing subsequent reaction. The major differences in the active sites between these two enzymes are the recognition mechanisms of the second substrates, 2-pyrone and DDG, respectively.

PubMed: 15213379
DOI: 10.1107/S0907444904008881

Experimental method

X-RAY DIFFRACTION (1.7 Å)