YME1_YEAST
ID YME1_YEAST Reviewed; 747 AA.
AC P32795; D6W434;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 194.
DE RecName: Full=Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1;
DE EC=3.4.24.-;
DE AltName: Full=Protein OSD1;
DE AltName: Full=Tat-binding homolog 11;
DE AltName: Full=Yeast mitochondrial escape protein 1;
GN Name=YME1; Synonyms=OSD1, YTA11; OrderedLocusNames=YPR024W;
GN ORFNames=YP9367.04;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBCELLULAR LOCATION, AND DISRUPTION
RP PHENOTYPE.
RX PubMed=8355690; DOI=10.1128/mcb.13.9.5418-5426.1993;
RA Thorsness P.E., White K.H., Fox T.D.;
RT "Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of
RT putative ATPase-encoding genes, causes increased escape of DNA from
RT mitochondria in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 13:5418-5426(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=7754704; DOI=10.1002/yea.320100903;
RA Schnall R., Mannhaupt G., Stucka R., Tauer R., Ehnle S., Schwarzlose C.,
RA Vetter I., Feldmann H.;
RT "Identification of a set of yeast genes coding for a novel family of
RT putative ATPases with high similarity to constituents of the 26S protease
RT complex.";
RL Yeast 10:1141-1155(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 24657 / D273-10B;
RX PubMed=7623837; DOI=10.1128/mcb.15.8.4441;
RA Nakai T., Yasuhara T., Fujiki Y., Ohashi A.;
RT "Multiple genes, including a member of the AAA family, are essential for
RT degradation of unassembled subunit 2 of cytochrome c oxidase in yeast
RT mitochondria.";
RL Mol. Cell. Biol. 15:4441-4452(1995).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169875;
RA Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
RA Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D.,
RA Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E.,
RA Churcher C.M., Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H.,
RA DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N.,
RA Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K.,
RA Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M.,
RA Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A.,
RA Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S.,
RA Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
RA Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
RA Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
RA Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
RA Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R.,
RA Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A.,
RA Vo D.H., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
RL Nature 387:103-105(1997).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [6]
RP SUBCELLULAR LOCATION, AND MUTAGENESIS OF LYS-327 AND GLU-541.
RX PubMed=8688560; DOI=10.1091/mbc.7.2.307;
RA Weber E.R., Hanekamp T., Thorsness P.E.;
RT "Biochemical and functional analysis of the YME1 gene product, an ATP and
RT zinc-dependent mitochondrial protease from S. cerevisiae.";
RL Mol. Biol. Cell 7:307-317(1996).
RN [7]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [8]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [9]
RP PROTEASE ACTIVITY, FUNCTION, SUBSTRATE-BINDING, AND MUTAGENESIS OF LYS-327;
RP TYR-354 AND GLU-381.
RX PubMed=16527490; DOI=10.1016/j.jsb.2006.01.009;
RA Graef M., Langer T.;
RT "Substrate specific consequences of central pore mutations in the i-AAA
RT protease Yme1 on substrate engagement.";
RL J. Struct. Biol. 156:101-108(2006).
RN [10]
RP FUNCTION, INTERACTION WITH MGR1, AND IDENTIFICATION IN THE I-AAA COMPLEX.
RX PubMed=16267274; DOI=10.1091/mbc.e05-06-0585;
RA Dunn C.D., Lee M.S., Spencer F.A., Jensen R.E.;
RT "A genomewide screen for petite-negative yeast strains yields a new subunit
RT of the i-AAA protease complex.";
RL Mol. Biol. Cell 17:213-226(2006).
RN [11]
RP SUBUNIT.
RX PubMed=18843051; DOI=10.1091/mbc.e08-01-0103;
RA Dunn C.D., Tamura Y., Sesaki H., Jensen R.E.;
RT "Mgr3p and Mgr1p are adaptors for the mitochondrial i-AAA protease
RT complex.";
RL Mol. Biol. Cell 19:5387-5397(2008).
CC -!- FUNCTION: Catalytic subunit of the mitochondrial inner membrane i-AAA
CC protease supercomplex required for mitochondrial inner membrane protein
CC turnover. The protease is probably ATP-dependent. Important to maintain
CC the integrity of the mitochondrial compartment. Required both for the
CC degradation of unassembled subunit 2 of cytochrome c oxidase (COX2) and
CC for efficient assembly of mitochondrial respiratory chain. Binds
CC unfolded substrates in an ATPase-independent manner; binding of folded
CC COX2, a physiological substrate, requires an active ATPase but when
CC COX2 is destabilized an active ATPase is no longer necessary.
CC {ECO:0000269|PubMed:16267274, ECO:0000269|PubMed:16527490}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250};
CC -!- SUBUNIT: Component of the mitochondrial inner membrane i-AAA protease
CC supercomplex composed of MGR1, MGR3 and YME1. Interacts directly with
CC MGR1. {ECO:0000269|PubMed:16267274, ECO:0000269|PubMed:18843051}.
CC -!- INTERACTION:
CC P32795; P25573: MGR1; NbExp=3; IntAct=EBI-27785, EBI-21740;
CC -!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
CC {ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:8355690,
CC ECO:0000269|PubMed:8688560}; Peripheral membrane protein
CC {ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:8355690,
CC ECO:0000269|PubMed:8688560}; Matrix side {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:8355690, ECO:0000269|PubMed:8688560}. Note=Although
CC this protein does not have any predicted transmembrane helices it
CC behaves like an integral membrane protein.
CC -!- DISRUPTION PHENOTYPE: An increased rate of escape of mtDNA to the
CC nucleus, no growth on nonfermentable carbon sources at 37 degrees
CC Celsius, a cold-sensitive defect in growth on fermentable carbon
CC sources, lethality in rho- (cytoplasmic petite) cells.
CC {ECO:0000269|PubMed:8355690}.
CC -!- MISCELLANEOUS: Present with 20100 molecules/cell in log phase SD
CC medium. {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the AAA ATPase
CC family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the peptidase M41
CC family. {ECO:0000305}.
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DR EMBL; L14616; AAA02883.1; -; Genomic_DNA.
DR EMBL; X81067; CAA56954.1; -; Genomic_DNA.
DR EMBL; D16332; BAA03839.1; -; Genomic_DNA.
DR EMBL; Z49274; CAA89278.1; -; Genomic_DNA.
DR EMBL; Z71255; CAA95020.1; -; Genomic_DNA.
DR EMBL; BK006949; DAA11450.1; -; Genomic_DNA.
DR PIR; S54498; S46608.
DR RefSeq; NP_015349.1; NM_001184121.1.
DR PDB; 2MV3; NMR; -; A=97-176.
DR PDBsum; 2MV3; -.
DR AlphaFoldDB; P32795; -.
DR SMR; P32795; -.
DR BioGRID; 36201; 760.
DR ComplexPortal; CPX-1655; i-AAA complex.
DR IntAct; P32795; 6.
DR STRING; 4932.YPR024W; -.
DR MEROPS; M41.004; -.
DR TCDB; 3.A.29.1.1; the mitochondrial inner membrane i-aaa protease complex (mimp) familly.
DR MaxQB; P32795; -.
DR PaxDb; P32795; -.
DR PRIDE; P32795; -.
DR EnsemblFungi; YPR024W_mRNA; YPR024W; YPR024W.
DR GeneID; 856135; -.
DR KEGG; sce:YPR024W; -.
DR SGD; S000006228; YME1.
DR VEuPathDB; FungiDB:YPR024W; -.
DR eggNOG; KOG0734; Eukaryota.
DR GeneTree; ENSGT00550000074836; -.
DR HOGENOM; CLU_000688_9_3_1; -.
DR InParanoid; P32795; -.
DR OMA; GFFTYIS; -.
DR BioCyc; YEAST:G3O-34184-MON; -.
DR BRENDA; 3.4.24.B19; 984.
DR PRO; PR:P32795; -.
DR Proteomes; UP000002311; Chromosome XVI.
DR RNAct; P32795; protein.
DR GO; GO:0031942; C:i-AAA complex; IDA:SGD.
DR GO; GO:0005743; C:mitochondrial inner membrane; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0004176; F:ATP-dependent peptidase activity; IMP:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro.
DR GO; GO:0007005; P:mitochondrion organization; IBA:GO_Central.
DR GO; GO:0030163; P:protein catabolic process; IMP:ComplexPortal.
DR GO; GO:0006457; P:protein folding; IMP:SGD.
DR GO; GO:0045041; P:protein import into mitochondrial intermembrane space; IDA:SGD.
DR GO; GO:0030150; P:protein import into mitochondrial matrix; IMP:SGD.
DR GO; GO:0051604; P:protein maturation; IMP:SGD.
DR GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IMP:SGD.
DR GO; GO:0006508; P:proteolysis; IBA:GO_Central.
DR Gene3D; 1.20.58.760; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_01458; FtsH; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR041569; AAA_lid_3.
DR InterPro; IPR003959; ATPase_AAA_core.
DR InterPro; IPR003960; ATPase_AAA_CS.
DR InterPro; IPR005936; FtsH.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR000642; Peptidase_M41.
DR InterPro; IPR037219; Peptidase_M41-like.
DR Pfam; PF00004; AAA; 1.
DR Pfam; PF17862; AAA_lid_3; 1.
DR Pfam; PF01434; Peptidase_M41; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF140990; SSF140990; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR01241; FtsH_fam; 1.
DR PROSITE; PS00674; AAA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Hydrolase; Membrane; Metal-binding;
KW Metalloprotease; Mitochondrion; Mitochondrion inner membrane;
KW Nucleotide-binding; Protease; Reference proteome; Zinc.
FT CHAIN 1..747
FT /note="Mitochondrial inner membrane i-AAA protease
FT supercomplex subunit YME1"
FT /id="PRO_0000084664"
FT REGION 51..92
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 718..747
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 51..66
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 67..92
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 725..739
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 541
FT /evidence="ECO:0000250"
FT BINDING 321..328
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT BINDING 540
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 544
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 618
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT MUTAGEN 327
FT /note="K->I,R,T: Does not complement a YME1 deletion
FT mutant, for K327R no longer binds or degrades COX2.
FT Probably has no ATPase activity."
FT /evidence="ECO:0000269|PubMed:16527490,
FT ECO:0000269|PubMed:8688560"
FT MUTAGEN 354
FT /note="Y->A,C,I,L,V: Partially complements a YME1 deletion
FT mutant."
FT /evidence="ECO:0000269|PubMed:16527490"
FT MUTAGEN 354
FT /note="Y->F,W: Complements a YME1 deletion mutant."
FT /evidence="ECO:0000269|PubMed:16527490"
FT MUTAGEN 354
FT /note="Y->K,N,R,T: Does not complement a YME1 deletion
FT mutant."
FT /evidence="ECO:0000269|PubMed:16527490"
FT MUTAGEN 354
FT /note="Y->S: Does not complement a YME1 deletion mutant,
FT retains 20% protease activity in vitro, binds an unfolded
FT hybrid substrate protein."
FT /evidence="ECO:0000269|PubMed:16527490"
FT MUTAGEN 381
FT /note="E->Q: Does not complement a YME1 deletion mutant, no
FT longer binds or degrades COX2. Probably has no ATPase
FT activity."
FT /evidence="ECO:0000269|PubMed:16527490"
FT MUTAGEN 541
FT /note="E->A,G,V: Does not complement a YME1 deletion
FT mutant, for E541A stabilizes otherwise unstable COX2."
FT /evidence="ECO:0000269|PubMed:8688560"
FT CONFLICT 52
FT /note="N -> T (in Ref. 2; CAA56954)"
FT /evidence="ECO:0000305"
FT CONFLICT 88
FT /note="T -> N (in Ref. 2; CAA56954)"
FT /evidence="ECO:0000305"
FT CONFLICT 584
FT /note="T -> A (in Ref. 3; BAA03839)"
FT /evidence="ECO:0000305"
FT HELIX 102..113
FT /evidence="ECO:0007829|PDB:2MV3"
FT HELIX 118..130
FT /evidence="ECO:0007829|PDB:2MV3"
FT HELIX 134..141
FT /evidence="ECO:0007829|PDB:2MV3"
FT HELIX 150..162
FT /evidence="ECO:0007829|PDB:2MV3"
FT HELIX 166..176
FT /evidence="ECO:0007829|PDB:2MV3"
SQ SEQUENCE 747 AA; 81772 MW; CA7C5C90097C4F8B CRC64;
MNVSKILVSP TVTTNVLRIF APRLPQIGAS LLVQKKWALR SKKFYRFYSE KNSGEMPPKK
EADSSGKASN KSTISSIDNS QPPPPSNTND KTKQANVAVS HAMLATREQE ANKDLTSPDA
QAAFYKLLLQ SNYPQYVVSR FETPGIASSP ECMELYMEAL QRIGRHSEAD AVRQNLLTAS
SAGAVNPSLA SSSSNQSGYH GNFPSMYSPL YGSRKEPLHV VVSESTFTVV SRWVKWLLVF
GILTYSFSEG FKYITENTTL LKSSEVADKS VDVAKTNVKF DDVCGCDEAR AELEEIVDFL
KDPTKYESLG GKLPKGVLLT GPPGTGKTLL ARATAGEAGV DFFFMSGSEF DEVYVGVGAK
RIRDLFAQAR SRAPAIIFID ELDAIGGKRN PKDQAYAKQT LNQLLVELDG FSQTSGIIII
GATNFPEALD KALTRPGRFD KVVNVDLPDV RGRADILKHH MKKITLADNV DPTIIARGTP
GLSGAELANL VNQAAVYACQ KNAVSVDMSH FEWAKDKILM GAERKTMVLT DAARKATAFH
EAGHAIMAKY TNGATPLYKA TILPRGRALG ITFQLPEMDK VDITKRECQA RLDVCMGGKI
AEELIYGKDN TTSGCGSDLQ SATGTARAMV TQYGMSDDVG PVNLSENWES WSNKIRDIAD
NEVIELLKDS EERARRLLTK KNVELHRLAQ GLIEYETLDA HEIEQVCKGE KLDKLKTSTN
TVVEGPDSDE RKDIGDDKPK IPTMLNA
