5CEE

Malic enzyme from Candidatus Phytoplasma AYWB in complex with NAD and Mg2+

Summary for 5CEE

• Entry DOI: 10.2210/pdb5cee/pdb
• Descriptor: NAD-dependent malic enzyme, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: phytoplasm malic enzyme, malate metabolism, plant pathogen, oxidoreductase
• Biological source: Aster yellows witches'-broom phytoplasma (strain AYWB)
• Total number of polymer chains: 1
• Total formula weight: 45006.35

Authors

Alvarez, C.E.,Trajtenberg, F.,Larrieux, N.,Saigo, M.,Mussi, M.A.,Andreo, C.S.,Drincovich, M.F.,Buschiazzo, A. (deposition date: 2015-07-06, release date: 2016-10-05, Last modification date: 2023-09-27)

Primary citation

Alvarez, C.E.,Trajtenberg, F.,Larrieux, N.,Saigo, M.,Golic, A.,Andreo, C.S.,Hogenhout, S.A.,Mussi, M.A.,Drincovich, M.F.,Buschiazzo, A.
The crystal structure of the malic enzyme from Candidatus Phytoplasma reveals the minimal structural determinants for a malic enzyme.
Acta Crystallogr D Struct Biol, 74:332-340, 2018

PubMed Abstract: Phytoplasmas are wall-less phytopathogenic bacteria that produce devastating effects in a wide variety of plants. Reductive evolution has shaped their genome, with the loss of many genes, limiting their metabolic capacities. Owing to the high concentration of C compounds in plants, and the presence of malic enzyme (ME) in all phytoplasma genomes so far sequenced, the oxidative decarboxylation of L-malate might represent an adaptation to generate energy. Aster yellows witches'-broom (Candidatus Phytoplasma) ME (AYWB-ME) is one of the smallest of all characterized MEs, yet retains full enzymatic activity. Here, the crystal structure of AYWB-ME is reported, revealing a unique fold that differs from those of `canonical' MEs. AYWB-ME is organized as a dimeric species formed by intertwining of the N-terminal domains of the protomers. As a consequence of such structural differences, key catalytic residues such as Tyr36 are positioned in the active site of each protomer but are provided by the other protomer of the dimer. A Tyr36Ala mutation abolishes the catalytic activity, indicating the key importance of this residue in the catalytic process but not in the dimeric assembly. Phylogenetic analyses suggest that larger MEs (large-subunit or chimeric MEs) might have evolved from this type of smaller scaffold by gaining small sequence cassettes or an entire functional domain. The Candidatus Phytoplasma AYWB-ME structure showcases a novel minimal structure design comprising a fully functional active site, making this enzyme an attractive starting point for rational genetic design.

PubMed: 29652260
DOI: 10.1107/S2059798318002759

Experimental method

X-RAY DIFFRACTION (2.498 Å)