3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme

MELISA LÁZARO; MIKEL VALLE; MARÍA-NATALIA LISA

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Simposio; Protein Data Bank Symposium - 50th year celebration; 2021

AMERICAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY

Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases (L-GDHs) composed of 180 kDa subunits (L-GDHs180) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs180 in the physiology of environmental and pathogenic bacteria, the lack of structural data for these enzymes has limited the progress of functional studies. We report the 3D structure of the mycobacterial L-GDH180 isoform from Mycobacterium smegmatis (mL-GDH180), obtained through an integrative approach that combined single-particle cryo-EM and X-ray protein crystallography. mL-GDH180 adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH180 involve a C-terminal domain that we propose as a new fold and a flexible N-terminal segment comprising ACT-like and PAS-type domains that could act as metabolic sensors. These findings reveal unique characteristics of domain organization and oligomeric assembly in the subfamily of L-GDHs, thus allowing to update the annotation of the Pfam family PF05088 that includes the L-GDHs180. Furthermore, our cryo-EM data evidenced fluctuations in the quaternary structure of mL-GDH180 that are possibly relevant for the allosteric regulation of the enzyme activity, uncovering unique aspects of the structure-function relationship in the L-GDHs subfamily.