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 22-FEB-2023, entry version 197. 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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; 762. 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) family. DR MaxQB; P32795; -. DR PaxDb; P32795; -. DR PeptideAtlas; P32795; -. DR EnsemblFungi; YPR024W_mRNA; YPR024W; YPR024W. DR GeneID; 856135; -. DR KEGG; sce:YPR024W; -. DR AGR; SGD:S000006228; -. 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 OrthoDB; 9585at2759; -. DR BioCyc; YEAST:G3O-34184-MON; -. DR BRENDA; 3.4.24.B19; 984. DR BioGRID-ORCS; 856135; 5 hits in 10 CRISPR screens. 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 CDD; cd00009; AAA; 1. DR Gene3D; 1.10.8.60; -; 1. DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1. DR Gene3D; 1.20.58.760; Peptidase M41; 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 PANTHER; PTHR23076:SF97; ATP-DEPENDENT ZINC METALLOPROTEASE YME1L1; 1. DR PANTHER; PTHR23076; METALLOPROTEASE M41 FTSH; 1. 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; FtsH protease domain-like; 1. DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 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 //