PDBsum entry 2mv3

Nucleotide binding protein

PDB id: 2mv3

Contents

Protein chain

88 a.a.

PDB id:

2mv3

Name:

Nucleotide binding protein

Title:

The n-domain of the aaa metalloproteinase yme1 from saccharomyces cerevisiae

Structure:

Mitochondrial inner membrane i-aaa protease supercomplex subunit yme1. Chain: a. Fragment: n-domain (unp residues 97-176). Synonym: protein osd1, tat-binding homolog 11, yeast mitochondrial escape protein 1, yme1-n. Engineered: yes

Source:

Saccharomyces cerevisiae s288c. Baker's yeast. Organism_taxid: 559292. Gene: yme1, osd1, yta11, ypr024w, yp9367.04. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

23 models

Authors:

F.Scharfenberg,J.Serek-Heuberger,J.Martin,A.N.Lupas,M.Coles

Key ref:

F.Scharfenberg et al. (2015). Structure and evolution of N-domains in AAA metalloproteases. J Mol Biol, 427, 910-923. PubMed id: 25576874 DOI: 10.1016/j.jmb.2014.12.024

Date:

22-Sep-14 Release date: 28-Jan-15

Protein chain

P32795  (YME1_YEAST) -  Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 747 a.a.

Struc: 88 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.24.- - ?????

DOI no: 10.1016/j.jmb.2014.12.024

J Mol Biol 427:910-923 (2015)

PubMed id: 25576874

Structure and evolution of N-domains in AAA metalloproteases.

F.Scharfenberg, J.Serek-Heuberger, M.Coles, M.D.Hartmann, M.Habeck, J.Martin, A.N.Lupas, V.Alva.

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.