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Protein

Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1

Gene

YME1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic subunit of the mitochondrial inner membrane i-AAA protease supercomplex required for mitochondrial inner membrane protein turnover. The protease is probably ATP-dependent. Important to maintain the integrity of the mitochondrial compartment. Required both for the degradation of unassembled subunit 2 of cytochrome c oxidase (COX2) and for efficient assembly of mitochondrial respiratory chain. Binds unfolded substrates in an ATPase-independent manner; binding of folded COX2, a physiological substrate, requires an active ATPase but when COX2 is destabilized an active ATPase is no longer necessary.2 Publications

Cofactori

Zn2+By similarityNote: Binds 1 zinc ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi540 – 5401Zinc; catalyticBy similarity
Active sitei541 – 5411By similarity
Metal bindingi544 – 5441Zinc; catalyticBy similarity
Metal bindingi618 – 6181Zinc; catalyticBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi321 – 3288ATPSequence analysis

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • ATP-dependent peptidase activity Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • metalloendopeptidase activity Source: InterPro
  • metallopeptidase activity Source: GO_Central

GO - Biological processi

  • misfolded or incompletely synthesized protein catabolic process Source: SGD
  • protein folding Source: SGD
  • protein import into mitochondrial intermembrane space Source: SGD
  • protein maturation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Metalloprotease, Protease

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-34184-MONOMER.
BRENDAi3.4.24.B19. 984.

Protein family/group databases

MEROPSiM41.004.

Names & Taxonomyi

Protein namesi
Recommended name:
Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 (EC:3.4.24.-)
Alternative name(s):
Protein OSD1
Tat-binding homolog 11
Yeast mitochondrial escape protein 1
Gene namesi
Name:YME1
Synonyms:OSD1, YTA11
Ordered Locus Names:YPR024W
ORF Names:YP9367.04
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPR024W.
SGDiS000006228. YME1.

Subcellular locationi

GO - Cellular componenti

  • i-AAA complex Source: SGD
  • mitochondrial inner membrane Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Membrane, Mitochondrion, Mitochondrion inner membrane

Pathology & Biotechi

Disruption phenotypei

An increased rate of escape of mtDNA to the nucleus, no growth on nonfermentable carbon sources at 37 degrees Celsius, a cold-sensitive defect in growth on fermentable carbon sources, lethality in rho- (cytoplasmic petite) cells.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi327 – 3271K → I, R or T: Does not complement a YME1 deletion mutant, for K327R no longer binds or degrades COX2. Probably has no ATPase activity. 2 Publications
Mutagenesisi354 – 3541Y → A, C, I, L or V: Partially complements a YME1 deletion mutant. 1 Publication
Mutagenesisi354 – 3541Y → F or W: Complements a YME1 deletion mutant. 1 Publication
Mutagenesisi354 – 3541Y → K, N, R or T: Does not complement a YME1 deletion mutant. 1 Publication
Mutagenesisi354 – 3541Y → S: Does not complement a YME1 deletion mutant, retains 20% protease activity in vitro, binds an unfolded hybrid substrate protein. 1 Publication
Mutagenesisi381 – 3811E → Q: Does not complement a YME1 deletion mutant, no longer binds or degrades COX2. Probably has no ATPase activity. 1 Publication
Mutagenesisi541 – 5411E → A, G or V: Does not complement a YME1 deletion mutant, for E541A stabilizes otherwise unstable COX2. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 747747Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1PRO_0000084664Add
BLAST

Proteomic databases

MaxQBiP32795.

Interactioni

Subunit structurei

Component of the mitochondrial inner membrane i-AAA protease supercomplex composed of MGR1, MGR3 and YME1. Interacts directly with MGR1.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
MGR1P255733EBI-27785,EBI-21740

Protein-protein interaction databases

BioGridi36201. 457 interactions.
IntActiP32795. 6 interactions.
MINTiMINT-4505879.

Structurei

Secondary structure

1
747
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi102 – 11312Combined sources
Helixi118 – 13013Combined sources
Helixi134 – 1418Combined sources
Helixi150 – 16213Combined sources
Helixi166 – 17611Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MV3NMR-A97-176[»]
ProteinModelPortaliP32795.
SMRiP32795. Positions 97-176, 278-710.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

In the N-terminal section; belongs to the AAA ATPase family.Curated
In the C-terminal section; belongs to the peptidase M41 family.Curated

Phylogenomic databases

GeneTreeiENSGT00550000074836.
HOGENOMiHOG000217276.
InParanoidiP32795.
KOiK08955.
OMAiVCMGGKI.
OrthoDBiEOG092C1LIZ.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_01458. FtsH. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR003960. ATPase_AAA_CS.
IPR005936. FtsH.
IPR027417. P-loop_NTPase.
IPR000642. Peptidase_M41.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
PF01434. Peptidase_M41. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR01241. FtsH_fam. 1 hit.
PROSITEiPS00674. AAA. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P32795-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNVSKILVSP TVTTNVLRIF APRLPQIGAS LLVQKKWALR SKKFYRFYSE
60 70 80 90 100
KNSGEMPPKK EADSSGKASN KSTISSIDNS QPPPPSNTND KTKQANVAVS
110 120 130 140 150
HAMLATREQE ANKDLTSPDA QAAFYKLLLQ SNYPQYVVSR FETPGIASSP
160 170 180 190 200
ECMELYMEAL QRIGRHSEAD AVRQNLLTAS SAGAVNPSLA SSSSNQSGYH
210 220 230 240 250
GNFPSMYSPL YGSRKEPLHV VVSESTFTVV SRWVKWLLVF GILTYSFSEG
260 270 280 290 300
FKYITENTTL LKSSEVADKS VDVAKTNVKF DDVCGCDEAR AELEEIVDFL
310 320 330 340 350
KDPTKYESLG GKLPKGVLLT GPPGTGKTLL ARATAGEAGV DFFFMSGSEF
360 370 380 390 400
DEVYVGVGAK RIRDLFAQAR SRAPAIIFID ELDAIGGKRN PKDQAYAKQT
410 420 430 440 450
LNQLLVELDG FSQTSGIIII GATNFPEALD KALTRPGRFD KVVNVDLPDV
460 470 480 490 500
RGRADILKHH MKKITLADNV DPTIIARGTP GLSGAELANL VNQAAVYACQ
510 520 530 540 550
KNAVSVDMSH FEWAKDKILM GAERKTMVLT DAARKATAFH EAGHAIMAKY
560 570 580 590 600
TNGATPLYKA TILPRGRALG ITFQLPEMDK VDITKRECQA RLDVCMGGKI
610 620 630 640 650
AEELIYGKDN TTSGCGSDLQ SATGTARAMV TQYGMSDDVG PVNLSENWES
660 670 680 690 700
WSNKIRDIAD NEVIELLKDS EERARRLLTK KNVELHRLAQ GLIEYETLDA
710 720 730 740
HEIEQVCKGE KLDKLKTSTN TVVEGPDSDE RKDIGDDKPK IPTMLNA
Length:747
Mass (Da):81,772
Last modified:October 1, 1993 - v1
Checksum:iCA7C5C90097C4F8B
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti52 – 521N → T in CAA56954 (PubMed:7754704).Curated
Sequence conflicti88 – 881T → N in CAA56954 (PubMed:7754704).Curated
Sequence conflicti584 – 5841T → A in BAA03839 (PubMed:7623837).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L14616 Genomic DNA. Translation: AAA02883.1.
X81067 Genomic DNA. Translation: CAA56954.1.
D16332 Genomic DNA. Translation: BAA03839.1.
Z49274 Genomic DNA. Translation: CAA89278.1.
Z71255 Genomic DNA. Translation: CAA95020.1.
BK006949 Genomic DNA. Translation: DAA11450.1.
PIRiS54498. S46608.
RefSeqiNP_015349.1. NM_001184121.1.

Genome annotation databases

EnsemblFungiiYPR024W; YPR024W; YPR024W.
GeneIDi856135.
KEGGisce:YPR024W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L14616 Genomic DNA. Translation: AAA02883.1.
X81067 Genomic DNA. Translation: CAA56954.1.
D16332 Genomic DNA. Translation: BAA03839.1.
Z49274 Genomic DNA. Translation: CAA89278.1.
Z71255 Genomic DNA. Translation: CAA95020.1.
BK006949 Genomic DNA. Translation: DAA11450.1.
PIRiS54498. S46608.
RefSeqiNP_015349.1. NM_001184121.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MV3NMR-A97-176[»]
ProteinModelPortaliP32795.
SMRiP32795. Positions 97-176, 278-710.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36201. 457 interactions.
IntActiP32795. 6 interactions.
MINTiMINT-4505879.

Protein family/group databases

MEROPSiM41.004.

Proteomic databases

MaxQBiP32795.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPR024W; YPR024W; YPR024W.
GeneIDi856135.
KEGGisce:YPR024W.

Organism-specific databases

EuPathDBiFungiDB:YPR024W.
SGDiS000006228. YME1.

Phylogenomic databases

GeneTreeiENSGT00550000074836.
HOGENOMiHOG000217276.
InParanoidiP32795.
KOiK08955.
OMAiVCMGGKI.
OrthoDBiEOG092C1LIZ.

Enzyme and pathway databases

BioCyciYEAST:G3O-34184-MONOMER.
BRENDAi3.4.24.B19. 984.

Miscellaneous databases

PROiP32795.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
HAMAPiMF_01458. FtsH. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR003959. ATPase_AAA_core.
IPR003960. ATPase_AAA_CS.
IPR005936. FtsH.
IPR027417. P-loop_NTPase.
IPR000642. Peptidase_M41.
[Graphical view]
PfamiPF00004. AAA. 1 hit.
PF01434. Peptidase_M41. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR01241. FtsH_fam. 1 hit.
PROSITEiPS00674. AAA. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYME1_YEAST
AccessioniPrimary (citable) accession number: P32795
Secondary accession number(s): D6W434
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1993
Last sequence update: October 1, 1993
Last modified: September 7, 2016
This is version 155 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 20100 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.