2MV3

The N-domain of the AAA metalloproteinase Yme1 from Saccharomyces cerevisiae

Summary for 2MV3

• Entry DOI: 10.2210/pdb2mv3/pdb
• Related: 2MUY
• NMR Information: BMRB: 25241
• Descriptor: Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 (1 entity in total)
• Functional Keywords: aaa atpase, substrate recognition domain, metalloprotease, nucleotide binding protein
• Biological source: Saccharomyces cerevisiae S288c (Baker's yeast)
• Cellular location: Mitochondrion inner membrane ; Peripheral membrane protein ; Matrix side : P32795
• Total number of polymer chains: 1
• Total formula weight: 10056.25

Authors

Scharfenberg, F.,Serek-Heuberger, J.,Martin, J.,Lupas, A.N.,Coles, M. (deposition date: 2014-09-22, release date: 2015-01-28, Last modification date: 2024-05-15)

Primary citation

Scharfenberg, F.,Serek-Heuberger, J.,Coles, M.,Hartmann, M.D.,Habeck, M.,Martin, J.,Lupas, A.N.,Alva, V.
Structure and Evolution of N-domains in AAA Metalloproteases.
J.Mol.Biol., 427:910-923, 2015

PubMed Abstract: Metalloproteases of the AAA (ATPases associated with various cellular activities) family play a crucial role in protein quality control within the cytoplasmic membrane of bacteria and the inner membrane of eukaryotic organelles. These membrane-anchored hexameric enzymes are composed of an N-terminal domain with one or two transmembrane helices, a central AAA ATPase module, and a C-terminal Zn(2+)-dependent protease. While the latter two domains have been well studied, so far, little is known about the N-terminal regions. Here, in an extensive bioinformatic and structural analysis, we identified three major, non-homologous groups of N-domains in AAA metalloproteases. By far, the largest one is the FtsH-like group of bacteria and eukaryotic organelles. The other two groups are specific to Yme1: one found in plants, fungi, and basal metazoans and the other one found exclusively in animals. Using NMR and crystallography, we determined the subunit structure and hexameric assembly of Escherichia coli FtsH-N, exhibiting an unusual α+β fold, and the conserved part of fungal Yme1-N from Saccharomyces cerevisiae, revealing a tetratricopeptide repeat fold. Our bioinformatic analysis showed that, uniquely among these proteins, the N-domain of Yme1 from the cnidarian Hydra vulgaris contains both the tetratricopeptide repeat region seen in basal metazoans and a region of homology to the N-domains of animals. Thus, it is a modern-day representative of an intermediate in the evolution of animal Yme1 from basal eukaryotic precursors.

PubMed: 25576874
DOI: 10.1016/j.jmb.2014.12.024

Experimental method

SOLUTION NMR