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DnaX + H2O
?
-
the enzyme partially degrades DnaX to produce stable fragments upon encountering a glycine-rich region adjacent to a structured domain
-
-
?
hybrid protein of subunit 2 of cytochrome oxidase residues 1-74, mouse dihydrofolate reductase, and mitochondrial presequence, residues 1-66, of subunit 9 of the ATPase of Neurospora crassa + H2O
4 peptide fragments f1-f4
-
in vitro import into the mitochondrion
product characterization
?
KAENQKARFSDVHGC + H2O
?
-
-
-
-
?
loosely folded Yta10(161)-dihydrofolate reductase + H2O
?
-
in vitro import into mitochondria, not intact wild-type dihydrofolate reductase
-
?
polynucleotide phosphorylase + H2O
?
-
Yme1 is required for PNPase assembly in the intermembrane space
-
-
?
prohibitin + H2O
?
-
-
-
-
?
protein Cox2 + H2O
?
-
degradation of membrane protein, essentially required as a membrane-integrated quality control
-
?
proteins + H2O
peptides
-
-
?
receptor protein Atg32 + H2O
?
-
-
-
-
?
residues 1-74 of subunit 2 of cytochrome oxidase + H2O
?
-
two-step procedure, in vitro import into the mitochondrion
-
?
subunit 2 of cytochrome c oxidase + H2O
?
-
-
-
-
?
unassembled cytochrome oxidase 2
?
-
-
-
?
unassembled gamma subunit of mitochondrial ATP-synthase + H2O
?
-
i.e. Atp3p
-
?
unassembled subunit II of cytochrome oxidase + H2O
?
-
i.e. Cox2p
-
?
Yta10(161)-DHFRmut + H2O
?
-
-
-
-
?
OPA1 + H2O
?
substrate is a dynamin-like GTPase
-
-
?
OPA1 + H2O
?
-
cleavage at protease site S2
-
-
?
OPA1 + H2O
?
-
YME1L cleaves OPA1 at S2
-
-
?
protein + H2O
peptides
-
activity depends on oligomerisation
-
?
protein + H2O
peptides
-
quality control system to selectively remove non-assembled polypeptides and to prevent their possible deleterious accumulation in the membrane, enzyme is crucial for viability
-
?
protein + H2O
peptides
-
ATP hydrolysis causes conformational changes, regulates the accessibility of the proteolytic sites and trigger unfolding of substrate polypeptides, substrate recognition and binding to the enzymes ATPase domain is crucial for proteolytic function against unfolded membrane protein substrates
product peptides are released directly into the intermembrane space
?
protein + H2O
peptides
-
enzyme probably forms a pore-like structure facilitating the transport of hydrophilic parts of the substrate protein during its extraction, limited substrate recognition, 25 amino acids of the substrate exposed to the solvent are sufficient for the enzyme to bind via its AAA domain
product peptides are released directly into the intermembrane space
?
protein + H2O
peptides
-
important role in the removal of non-assembled polypeptides from the inner membrane, inactivation of the enzyme is lethal, enzyme deficiency causes pleiotropic defects, including impaired respiration at high temperature and an aberrant mitochondrial morphology, required as a membrane-integrated quality control to facilitate protein folding and to ensure the selective removal of non-native polypeptides
-
?
protein + H2O
peptides
-
proteolytic activity of the i-AAA protease is required for the maintenance of mitochondrial function at high temperature, pointing to an important role in mitochondrial biogenesis
-
?
protein + H2O
peptides
-
the substrate binding region is mapped to the N-terminus of the AAA domain and is probably close to the membrane surface, degradation of membrane proteins, essentially required as a membrane-integrated quality control
-
?
Tim10 + H2O
?
-
i.e. translocase of inner membrane 10
-
-
?
Tim10 + H2O
?
-
i.e. translocase of inner membrane 10
-
-
?
Tim17-2 + H2O
?
substrate is an essential component of the mitochondrial TIM17:23 translocase
-
-
?
Tim17-2 + H2O
?
substrate is an essential component of the mitochondrial TIM17:23 translocase
-
-
?
Tim9 + H2O
?
-
i.e. translocase of inner membrane 9
-
-
?
Tim9 + H2O
?
-
i.e. translocase of inner membrane 9
-
-
?
Cox2 + H2O
?
additional information
-
-
-
-
?
membrane protein + H2O
?
additional information
-
proteolytic activity depends on the presence of hydrophobic amino acid residues at position 354 within the pore loop of Yme1
-
-
?
additional information
?
-
-
does not cleave subunit 2 of cytochrome c oxidase
-
-
?
additional information
?
-
-
shedding model for availability of water molecules: enzyme shed solvent exposed loops or domains from membrane-embedded polypeptides, pulling model: binding of unfolded substrate protein segments together with ATP-dependent conformational changes in the enzyme can provide a plling force on membrane proteins, with the enzyme being embedded in the bilayer
-
?
additional information
?
-
-
polynucleotide phosphorylase-dihydrofolate reductase is not a proteolytic substrate for Yme1
-
-
?
additional information
?
-
Yme1 probably chaperones the folding and/or assembly of Oxa1-exported Cox2 (cytochrome c oxidase subunit) in the absence of Mrg1 or Mgr3
-
-
?
additional information
?
-
-
Yme1 probably chaperones the folding and/or assembly of Oxa1-exported Cox2 (cytochrome c oxidase subunit) in the absence of Mrg1 or Mgr3
-
-
?
additional information
?
-
-
YME1L degradation involves the activity of the ATP-independent mitochondrial protease OMA1
-
-
?
additional information
?
-
-
primary function of Tim9 is to protect Tim10 from degradation by Yme1 via assembly into the Tim9-Tim10 complex
-
-
?
additional information
?
-
-
Yme1p degrades Tim10 more rapidly than Tim9, and loss of Tim10 is accelerated by disruption of conserved disulfide bonds within the substrate. An unstructured N-terminal region of Tim10 is necessary and sufficient to target the substrate to the protease through recognition of a short phenylalanine rich motif
-
-
?
additional information
?
-
-
primary function of Tim9 is to protect Tim10 from degradation by Yme1 via assembly into the Tim9-Tim10 complex
-
-
?
Yta10(1-161)-DHFRmut + H2O
?
additional information
-
-
-
-
?
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metabolism
-
constitutive OPA1 cleavage by YME1L and OMA1 at two distinct sites leads to the accumulation of both long and short forms of OPA1 and maintains mitochondrial fusion
malfunction
-
a IAP deletion strain is neither impaired in viability, nor does it show any changes in morphology under standard growth conditions (20°C) but shows increased lifespan and is sensitive to elevated temperature (37°C). Deletion of IAP affects the composition of the mitochondrial respiratory chain complexes
malfunction
-
mutations in the catalytic subunit of the i-AAA protease complex cause an elevated rate of mitochondrial turnover. Inactivation of the enzyme results in a slight increase in H2O2 sensitivity; while inactivation of both TAZ1 and YME1 together results in a dramatic increase in H2O2 sensitivity
malfunction
-
mutations in the catalytic subunit of the i-AAA protease complex cause an elevated rate of mitochondrial turnover. Inactivation of the enzyme results in a slight increase in H2O2 sensitivity; while inactivation of both TAZ1 and YME1 together results in a dramatic increase in H2O2 sensitivity
-
physiological function
-
stress-induced YME1L degradation attenuates protective regulation of mitochondrial proteostasis and promotes cellular death in response to oxidative stress
physiological function
-
the mitochondrial i-AAA protease Yme1 mediates Atg32 processing and is required for mitophagy. The enzyme regulates the Atg32-Atg11 interaction
physiological function
-
the protease Yme1 is required for efficient mitophagy in the absence of tafazzin. The catalytic subunit of the i-AAA protease complex is responsible for degradation of unfolded or misfolded mitochondrial gene products and also has a role in intermembrane space protein folding
physiological function
-
Yme1 has a folding assistant function for dihydrofolate reductase in the intermembrane space, in addition to its proteolytic function, in the protein homeostasis of mitochondria
physiological function
abundance of the Tim17-2 protein, an essential component of the TIM17:23 translocase, is directly controlled by the proteolytic activity of FTSH4. Plants that are lacking functional FTSH4 protease display a significantly enhanced capacity of preprotein import through the TIM17:23-dependent pathway
physiological function
both m-AAA and i-AAA complexes coordinately regulate OMA1 processing and turnover, and consequently control which OPA1 isoforms are present
physiological function
mice lacking YME1L in the nervous system manifest ocular dysfunction with microphthalmia and cataracts and develop deficiencies in locomotor activity due to specific degeneration of spinal cord axons. Mitochondrial fragmentation occurs throughout the nervous system and does not correlate with the degenerative phenotype. Deletion of metalloprotease Oma1 restores tubular mitochondria but deteriorates axonal degeneration in the absence of YME1L
physiological function
YME1L-deficient mice manifest ocular dysfunction with microphthalmia and cataracts and develop deficiencies in locomotor activity due to specific degeneration of spinal cord axons, which relay proprioceptive signals from the hind limbs to the cerebellum. Mitochondrial fragmentation occurs throughout the nervous system and does not correlate with the degenerative phenotype. Deletion of metalloendopeptidase Oma1 restores tubular mitochondria but deteriorates axonal degeneration in the absence of YME1L
physiological function
-
the protease Yme1 is required for efficient mitophagy in the absence of tafazzin. The catalytic subunit of the i-AAA protease complex is responsible for degradation of unfolded or misfolded mitochondrial gene products and also has a role in intermembrane space protein folding
-
physiological function
-
abundance of the Tim17-2 protein, an essential component of the TIM17:23 translocase, is directly controlled by the proteolytic activity of FTSH4. Plants that are lacking functional FTSH4 protease display a significantly enhanced capacity of preprotein import through the TIM17:23-dependent pathway
-
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K327R
-
point mutation at the ATP-binding site, catalytically inactive
H486Y
inactive
E541Q
-
point mutation, inactive
E541Q
-
proteolytically inactive
E541Q
-
site-directed mutagenesis, exchange in the active site, no complementation of deficient mutant cell DELTAyme1
E541Q
additional information
-
efficiently precipitates Yta10(1-161)-DHFRmut
additional information
additional information
-
mutants of Yme1, which harbour aromatic, aliphatic, polar and charged residues at position 354 of Yme1, accumulate at similar levels in mitochondria as wild type, when expressed in deltayme1 yeast strain under the control of the endogenous Yme1 promoter, whereas deltayme1 cells do not grow on non-fermentable carbon sources at elevated temperature. Cell growth is restored upon expression of wild type Yme1 harbouring a tyrosine residue at position 354. Replacement by phenylalanine or tryptophan does not impair cell growth under these conditions. The introduction of aliphatic residues allows cell growth to a different extent, improved cell growth with increasing hydrophobicity of the aliphatic amino acids, polar or charged amino acid residues do not support respiratory growth
additional information
additional information
-
mutation in the Walker A- or Walker B-motif within the AAA domain strongly impairs the association of newly synthesized Cox2 with Yme1
Y354S
additional information
-
weak activity against Cox2, precipitates Yta10(1-161)-DHFRmut
Y354T
additional information
-
weak activity against Cox2
Y354W
additional information
-
fully restored respiratory growth, only partial activity against Cox2
additional information
-
construction of inactive mutant by site-directed mutagenesis in the ATP and Zn2+ binding domains, inactivation of the enzyme causes several distinct phenotypes: an increased rate of DNA escape from mitochondria, temperature-sensitive growth on nonfermentable carbon sources, extremely slow growth when mitochondrial DNA is completely absent from the cell, and altered morphology of the mitochondrial compartment
additional information
-
inactivation of the enzyme causes pleiotropic defects, including impaired respiration and aberrant mitochondrial morphology
additional information
-
N-terminal AAA-domain fragment, expressed in Escherichia coli, is sufficient for substrate binding, but the efficiency is reduced by 5fold compared to the wild-type enzyme
additional information
-
yme1delta mutant with Nde1p-HA turnover defect, mgr1delta yme1delta double mutant indistinguishable from the yme1delta mutant
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Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M.C.; Estreicher, A.; Gasteiger, E.; Martin M.J.; Michoud, K.; O'Donovan, C.; Phan, I.; Pilbout, S.; Schneider, M.
The SWISS-PROT protein knowledgebase and its supplement TrEMBL
Nucleic Acids Res.
31
365-370
2003
Saccharomyces cerevisiae (P32795)
brenda
Langer, T.; Kaser, M.; Klanner, C.; Leonhard, K.
AAA proteases of mitochondria: quality control of membrane proteins and regulatory functions during mitochondrial biogenesis
Biochem. Soc. Trans.
29
431-436
2001
Saccharomyces cerevisiae, Neurospora crassa
brenda
Leonhard, K.; Herrmann, J.M.; Stuart, R.A.; Mannhaupt, G.; Neupert, W.; Langer, T.
AAA proteases with catalytic sites on opposite membrane surfaces comprise a proteolytic system for the ATP-dependent degradation of inner membrane proteins in mitochondria
EMBO J.
15
4218-4229
1996
Saccharomyces cerevisiae
brenda
Weber, E.R.; Hanekamp, T.; Thorsness, P.E.
Biochemical and functional analysis of the YME1 gene product, an ATP and zinc-dependent mitochondrial protease from S. cerevisiae
Mol. Biol. Cell
7
307-317
1996
Saccharomyces cerevisiae
brenda
Leonhard, K.; Stiegler, A.; Neupert, W.; Langer, T.
Chaperone-like activity of the AAA domain of the yeast Yme1 AAA protease
Nature
398
348-351
1999
Saccharomyces cerevisiae
brenda
Graef, M.; Langer, T.
Substrate specific consequences of central pore mutations in the i-AAA protease Yme1 on substrate engagement
J. Struct. Biol.
156
101-108
2006
More
brenda
Dunn, C.D.; Lee, M.S.; Spencer, F.A.; Jensen, R.E.
A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex
Mol. Biol. Cell
17
213-226
2006
Saccharomyces cerevisiae
brenda
Arnold, I.; Wagner-Ecker, M.; Ansorge, W.; Langer, T.
Evidence for a novel mitochondria-to-nucleus signalling pathway in respiring cells lacking i-AAA protease and the ABC-transporter Mdl1
Gene
367
74-88
2006
Saccharomyces cerevisiae, Saccharomyces cerevisiae W303-1A
brenda
Song, Z.; Chen, H.; Fiket, M.; Alexander, C.; Chan, D.C.
OPA1 processing controls mitochondrial fusion and is regulated by mRNA splicing, membrane potential, and Yme1L
J. Cell Biol.
178
749-755
2007
Saccharomyces cerevisiae
brenda
Rainey, R.N.; Glavin, J.D.; Chen, H.W.; French, S.W.; Teitell, M.A.; Koehler, C.M.
A new function in translocation for the mitochondrial i-AAA protease Yme1: import of polynucleotide phosphorylase into the intermembrane space
Mol. Cell. Biol.
26
8488-8497
2006
Saccharomyces cerevisiae
brenda
Graef, M.; Seewald, G.; Langer, T.
Substrate recognition by AAA+ ATPases: distinct substrate binding modes in ATP-dependent protease Yme1 of the mitochondrial intermembrane space
Mol. Cell. Biol.
27
2476-2485
2007
Saccharomyces cerevisiae, Neurospora crassa
brenda
Fiumera, H.L.; Dunham, M.J.; Saracco, S.A.; Butler, C.A.; Kelly, J.A.; Fox, T.D.
Translocation and assembly of mitochondrially coded Saccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1 in the absence of Cox18
Genetics
182
519-528
2009
Saccharomyces cerevisiae (P32795), Saccharomyces cerevisiae
brenda
Dunn, C.D.; Tamura, Y.; Sesaki, H.; Jensen, R.E.
Mgr3p and Mgr1p are adaptors for the mitochondrial i-AAA protease complex
Mol. Biol. Cell
19
5387-5397
2008
Saccharomyces cerevisiae (P32795), Saccharomyces cerevisiae
brenda
Weil, A.; Luce, K.; Droese, S.; Wittig, I.; Brandt, U.; Osiewacz, H.D.
Unmasking a temperature-dependent effect of the P. anserina i-AAA protease on aging and development
Cell Cycle
10
4280-4290
2011
Podospora anserina
brenda
Wang, K.; Jin, M.; Liu, X.; Klionsky, D.J.
Proteolytic processing of Atg32 by the mitochondrial i-AAA protease Yme1 regulates mitophagy
Autophagy
9
1828-1836
2013
Saccharomyces cerevisiae
brenda
Rainbolt, T.K.; Saunders, J.M.; Wiseman, R.L.
YME1L degradation reduces mitochondrial proteolytic capacity during oxidative stress
EMBO Rep.
16
97-106
2015
Saccharomyces cerevisiae
brenda
Gaspard, G.J.; McMaster, C.R.
The mitochondrial quality control protein Yme1 is necessary to prevent defective mitophagy in a yeast model of Barth syndrome
J. Biol. Chem.
290
9284-9298
2015
Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4741
brenda
Anand, R.; Wai, T.; Baker, M.J.; Kladt, N.; Schauss, A.C.; Rugarli, E.; Langer, T.
The i-AAA protease YME1L and OMA1 cleave OPA1 to balance mitochondrial fusion and fission
J. Cell Biol.
204
919-929
2014
Saccharomyces cerevisiae
brenda
Schreiner, B.; Westerburg, H.; Forne, I.; Imhof, A.; Neupert, W.; Mokranjac, D.
Role of the AAA protease Yme1 in folding of proteins in the intermembrane space of mitochondria
Mol. Biol. Cell
23
4335-4346
2012
Saccharomyces cerevisiae
brenda
Vass, R.H.; Chien, P.
Critical clamp loader processing by an essential AAA+ protease in Caulobacter crescentus
Proc. Natl. Acad. Sci. USA
110
18138-18143
2013
Caulobacter vibrioides
brenda
Spiller, M.; Guo, L.; Wang, Q.; Tran, P.; Lu, H.
Mitochondrial Tim9 protects Tim10 from degradation by the protease Yme1
Biosci. Rep.
35
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2015
Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4742
brenda
Sprenger, H.; Wani, G.; Hesseling, A.; Koenig, T.; Patron, M.; MacVicar, T.; Ahola, S.; Wai, T.; Barth, E.; Rugarli, E.; Bergami, M.; Langer, T.
Loss of the mitochondrial i-AAA protease YME1L leads to ocular dysfunction and spinal axonopathy
EMBO Mol. Med.
11
e9288
2019
Mus musculus (O88967)
brenda
Wai, T.; Saita, S.; Nolte, H.; Mueller, S.; Koenig, T.; Richter-Dennerlein, R.; Sprenger, H.G.; Madrenas, J.; Muehlmeister, M.; Brandt, U.; Krueger, M.; Langer, T.
The membrane scaffold SLP2 anchors a proteolytic hub in mitochondria containing PARL and the i-AAA protease YME1L
EMBO Rep.
17
1844-1856
2016
Mus musculus (O88967)
brenda
Opalinska, M.; Parys, K.; Murcha, M.W.; Janska, H.
The plant i-AAA protease controls the turnover of an essential mitochondrial protein import component
J. Cell Sci.
131
jcs200733
2018
Arabidopsis thaliana (O80983), Arabidopsis thaliana Col-0 (O80983)
brenda
Consolato, F.; Maltecca, F.; Tulli, S.; Sambri, I.; Casari, G.
m-AAA and i-AAA complexes coordinate to regulate OMA1, the stress-activated supervisor of mitochondrial dynamics
J. Cell Sci.
131
jcs213546
2018
Mus musculus (O88967)
brenda
Rampello, A.J.; Glynn, S.E.
Identification of a degradation signal sequence within substrates of the mitochondrial i-AAA protease
J. Mol. Biol.
429
873-885
2017
Saccharomyces cerevisiae
brenda