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Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1 (EC 3.4.24.-) (Protein OSD1) (Tat-binding homolog 11) (Yeast mitochondrial escape protein 1)

 YME1_YEAST              Reviewed;         747 AA.
P32795; D6W434;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
01-OCT-1993, sequence version 1.
12-SEP-2018, entry version 174.
RecName: Full=Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1;
EC=3.4.24.-;
AltName: Full=Protein OSD1;
AltName: Full=Tat-binding homolog 11;
AltName: Full=Yeast mitochondrial escape protein 1;
Name=YME1; Synonyms=OSD1, YTA11; OrderedLocusNames=YPR024W;
ORFNames=YP9367.04;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], SUBCELLULAR LOCATION, AND
DISRUPTION PHENOTYPE.
PubMed=8355690; DOI=10.1128/MCB.13.9.5418;
Thorsness P.E., White K.H., Fox T.D.;
"Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of
putative ATPase-encoding genes, causes increased escape of DNA from
mitochondria in Saccharomyces cerevisiae.";
Mol. Cell. Biol. 13:5418-5426(1993).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=7754704; DOI=10.1002/yea.320100903;
Schnall R., Mannhaupt G., Stucka R., Tauer R., Ehnle S.,
Schwarzlose C., Vetter I., Feldmann H.;
"Identification of a set of yeast genes coding for a novel family of
putative ATPases with high similarity to constituents of the 26S
protease complex.";
Yeast 10:1141-1155(1994).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 24657 / D273-10B;
PubMed=7623837; DOI=10.1128/MCB.15.8.4441;
Nakai T., Yasuhara T., Fujiki Y., Ohashi A.;
"Multiple genes, including a member of the AAA family, are essential
for degradation of unassembled subunit 2 of cytochrome c oxidase in
yeast mitochondria.";
Mol. Cell. Biol. 15:4441-4452(1995).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169875;
Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W.,
Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V.,
Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M.,
Chung E., Churcher C.M., Coster F., Davis K., Davis R.W.,
Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A.,
Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A.,
Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W.,
Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K.,
Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J.,
Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D.,
Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D.,
Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S.,
Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B.,
Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A.,
Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V.,
Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W.,
Zollner A., Vo D.H., Hani J.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.";
Nature 387:103-105(1997).
[5]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[6]
SUBCELLULAR LOCATION, AND MUTAGENESIS OF LYS-327 AND GLU-541.
PubMed=8688560; DOI=10.1091/mbc.7.2.307;
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).
[7]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[8]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[9]
PROTEASE ACTIVITY, FUNCTION, SUBSTRATE-BINDING, AND MUTAGENESIS OF
LYS-327; TYR-354 AND GLU-381.
PubMed=16527490; DOI=10.1016/j.jsb.2006.01.009;
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).
[10]
FUNCTION, INTERACTION WITH MGR1, AND IDENTIFICATION IN THE I-AAA
COMPLEX.
PubMed=16267274; DOI=10.1091/mbc.E05-06-0585;
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).
[11]
SUBUNIT.
PubMed=18843051; DOI=10.1091/mbc.E08-01-0103;
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).
-!- FUNCTION: 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.
{ECO:0000269|PubMed:16267274, ECO:0000269|PubMed:16527490}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
Note=Binds 1 zinc ion per subunit. {ECO:0000250};
-!- SUBUNIT: Component of the mitochondrial inner membrane i-AAA
protease supercomplex composed of MGR1, MGR3 and YME1. Interacts
directly with MGR1. {ECO:0000269|PubMed:16267274,
ECO:0000269|PubMed:18843051}.
-!- INTERACTION:
P25573:MGR1; NbExp=3; IntAct=EBI-27785, EBI-21740;
-!- SUBCELLULAR LOCATION: Mitochondrion inner membrane
{ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:8355690,
ECO:0000269|PubMed:8688560}; Peripheral membrane protein
{ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:8355690,
ECO:0000269|PubMed:8688560}; Matrix side
{ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:8355690,
ECO:0000269|PubMed:8688560}. Note=Although this protein does not
have any predicted transmembrane helices it behaves like an
integral membrane protein.
-!- DISRUPTION PHENOTYPE: 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.
{ECO:0000269|PubMed:8355690}.
-!- MISCELLANEOUS: Present with 20100 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: In the N-terminal section; belongs to the AAA ATPase
family. {ECO:0000305}.
-!- SIMILARITY: In the C-terminal section; belongs to the peptidase
M41 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; L14616; AAA02883.1; -; Genomic_DNA.
EMBL; X81067; CAA56954.1; -; Genomic_DNA.
EMBL; D16332; BAA03839.1; -; Genomic_DNA.
EMBL; Z49274; CAA89278.1; -; Genomic_DNA.
EMBL; Z71255; CAA95020.1; -; Genomic_DNA.
EMBL; BK006949; DAA11450.1; -; Genomic_DNA.
PIR; S54498; S46608.
RefSeq; NP_015349.1; NM_001184121.1.
PDB; 2MV3; NMR; -; A=97-176.
PDBsum; 2MV3; -.
ProteinModelPortal; P32795; -.
SMR; P32795; -.
BioGrid; 36201; 749.
ComplexPortal; CPX-1655; i-AAA complex.
IntAct; P32795; 6.
STRING; 4932.YPR024W; -.
MEROPS; M41.004; -.
TCDB; 3.A.29.1.1; the mitochondrial inner membrane i-aaa protease complex (mimp) familly.
MaxQB; P32795; -.
PaxDb; P32795; -.
PRIDE; P32795; -.
EnsemblFungi; YPR024W; YPR024W; YPR024W.
GeneID; 856135; -.
KEGG; sce:YPR024W; -.
EuPathDB; FungiDB:YPR024W; -.
SGD; S000006228; YME1.
GeneTree; ENSGT00550000074836; -.
HOGENOM; HOG000217276; -.
InParanoid; P32795; -.
KO; K08955; -.
OMA; FRWVKFL; -.
OrthoDB; EOG092C1LIZ; -.
BioCyc; YEAST:G3O-34184-MONOMER; -.
BRENDA; 3.4.24.B19; 984.
PRO; PR:P32795; -.
Proteomes; UP000002311; Chromosome XVI.
GO; GO:0031942; C:i-AAA complex; IDA:SGD.
GO; GO:0005743; C:mitochondrial inner membrane; IDA:SGD.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004176; F:ATP-dependent peptidase activity; IMP:SGD.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro.
GO; GO:0008237; F:metallopeptidase activity; IBA:GO_Central.
GO; GO:0006457; P:protein folding; IMP:SGD.
GO; GO:0045041; P:protein import into mitochondrial intermembrane space; IDA:SGD.
GO; GO:0030150; P:protein import into mitochondrial matrix; IMP:SGD.
GO; GO:0051604; P:protein maturation; IMP:SGD.
GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IMP:SGD.
HAMAP; MF_01458; FtsH; 1.
InterPro; IPR003593; AAA+_ATPase.
InterPro; IPR003959; ATPase_AAA_core.
InterPro; IPR003960; ATPase_AAA_CS.
InterPro; IPR005936; FtsH.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR000642; Peptidase_M41.
InterPro; IPR037219; Peptidase_M41-like.
Pfam; PF00004; AAA; 1.
Pfam; PF01434; Peptidase_M41; 1.
SMART; SM00382; AAA; 1.
SUPFAM; SSF140990; SSF140990; 1.
SUPFAM; SSF52540; SSF52540; 1.
TIGRFAMs; TIGR01241; FtsH_fam; 1.
PROSITE; PS00674; AAA; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Complete proteome; Hydrolase; Membrane;
Metal-binding; Metalloprotease; Mitochondrion;
Mitochondrion inner membrane; Nucleotide-binding; Protease;
Reference proteome; Zinc.
CHAIN 1 747 Mitochondrial inner membrane i-AAA
protease supercomplex subunit YME1.
/FTId=PRO_0000084664.
NP_BIND 321 328 ATP. {ECO:0000255}.
ACT_SITE 541 541 {ECO:0000250}.
METAL 540 540 Zinc; catalytic. {ECO:0000250}.
METAL 544 544 Zinc; catalytic. {ECO:0000250}.
METAL 618 618 Zinc; catalytic. {ECO:0000250}.
MUTAGEN 327 327 K->I,R,T: Does not complement a YME1
deletion mutant, for K327R no longer
binds or degrades COX2. Probably has no
ATPase activity.
{ECO:0000269|PubMed:16527490,
ECO:0000269|PubMed:8688560}.
MUTAGEN 354 354 Y->A,C,I,L,V: Partially complements a
YME1 deletion mutant.
{ECO:0000269|PubMed:16527490}.
MUTAGEN 354 354 Y->F,W: Complements a YME1 deletion
mutant. {ECO:0000269|PubMed:16527490}.
MUTAGEN 354 354 Y->K,N,R,T: Does not complement a YME1
deletion mutant.
{ECO:0000269|PubMed:16527490}.
MUTAGEN 354 354 Y->S: Does not complement a YME1 deletion
mutant, retains 20% protease activity in
vitro, binds an unfolded hybrid substrate
protein. {ECO:0000269|PubMed:16527490}.
MUTAGEN 381 381 E->Q: Does not complement a YME1 deletion
mutant, no longer binds or degrades COX2.
Probably has no ATPase activity.
{ECO:0000269|PubMed:16527490}.
MUTAGEN 541 541 E->A,G,V: Does not complement a YME1
deletion mutant, for E541A stabilizes
otherwise unstable COX2.
{ECO:0000269|PubMed:8688560}.
CONFLICT 52 52 N -> T (in Ref. 2; CAA56954).
{ECO:0000305}.
CONFLICT 88 88 T -> N (in Ref. 2; CAA56954).
{ECO:0000305}.
CONFLICT 584 584 T -> A (in Ref. 3; BAA03839).
{ECO:0000305}.
HELIX 102 113 {ECO:0000244|PDB:2MV3}.
HELIX 118 130 {ECO:0000244|PDB:2MV3}.
HELIX 134 141 {ECO:0000244|PDB:2MV3}.
HELIX 150 162 {ECO:0000244|PDB:2MV3}.
HELIX 166 176 {ECO:0000244|PDB:2MV3}.
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


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