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PMIP_YEAST
ID   PMIP_YEAST              Reviewed;         772 AA.
AC   P35999; D6VX62; P51980;
DT   01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 2.
DT   03-AUG-2022, entry version 179.
DE   RecName: Full=Mitochondrial intermediate peptidase;
DE            Short=MIP;
DE            EC=3.4.24.59;
DE   Flags: Precursor;
GN   Name=OCT1; Synonyms=MIP1; OrderedLocusNames=YKL134C;
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], AND FUNCTION.
RX   PubMed=8035833; DOI=10.1128/mcb.14.8.5603-5616.1994;
RA   Isaya G., Miklos D., Rollins R.A.;
RT   "MIP1, a new yeast gene homologous to the rat mitochondrial intermediate
RT   peptidase gene, is required for oxidative metabolism in Saccharomyces
RT   cerevisiae.";
RL   Mol. Cell. Biol. 14:5603-5616(1994).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=8196765; DOI=10.1038/369371a0;
RA   Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V.,
RA   Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P.,
RA   Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L.,
RA   Daignan-Fornier B., del Rey F., Dion C., Domdey H., Duesterhoeft A.,
RA   Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H.,
RA   Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L.,
RA   Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M.,
RA   Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H.,
RA   Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J.,
RA   Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H.,
RA   Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J.,
RA   Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S.,
RA   Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F.,
RA   Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R.,
RA   Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W.,
RA   Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M.,
RA   Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C.,
RA   Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H.,
RA   Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L.,
RA   van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S.,
RA   von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M.,
RA   Becker I., Mewes H.-W.;
RT   "Complete DNA sequence of yeast chromosome XI.";
RL   Nature 369:371-378(1994).
RN   [3]
RP   GENOME REANNOTATION, AND SEQUENCE REVISION TO 343-350 AND 694-702.
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   [4]
RP   FUNCTION.
RX   PubMed=7593000; DOI=10.1074/jbc.270.45.27366;
RA   Branda S.S., Isaya G.;
RT   "Prediction and identification of new natural substrates of the yeast
RT   mitochondrial intermediate peptidase.";
RL   J. Biol. Chem. 270:27366-27373(1995).
RN   [5]
RP   MUTAGENESIS OF CYS-131; PHE-557; HIS-558; GLU-559; GLY-561; HIS-562;
RP   HIS-565; GLY-578; CYS-581; ASP-584; GLU-587; PRO-589; SER-590 AND GLU-594,
RP   AND SUBCELLULAR LOCATION.
RX   PubMed=8831696; DOI=10.1006/bbrc.1996.1435;
RA   Chew A., Rollins R.A., Sakati W.R., Isaya G.;
RT   "Mutations in a putative zinc-binding domain inactivate the mitochondrial
RT   intermediate peptidase.";
RL   Biochem. Biophys. Res. Commun. 226:822-829(1996).
RN   [6]
RP   ACTIVITY REGULATION.
RX   PubMed=10332043; DOI=10.1093/hmg/8.6.1099;
RA   Branda S.S., Yang Z.Y., Chew A., Isaya G.;
RT   "Mitochondrial intermediate peptidase and the yeast frataxin homolog
RT   together maintain mitochondrial iron homeostasis in Saccharomyces
RT   cerevisiae.";
RL   Hum. Mol. Genet. 8:1099-1110(1999).
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   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
RP   SPECTROMETRY.
RX   PubMed=16823961; DOI=10.1021/pr050477f;
RA   Reinders J., Zahedi R.P., Pfanner N., Meisinger C., Sickmann A.;
RT   "Toward the complete yeast mitochondrial proteome: multidimensional
RT   separation techniques for mitochondrial proteomics.";
RL   J. Proteome Res. 5:1543-1554(2006).
CC   -!- FUNCTION: Cleaves proteins, imported into the mitochondrion, to their
CC       mature size. While most mitochondrial precursor proteins are processed
CC       to the mature form in one step by mitochondrial processing peptidase
CC       (MPP), the sequential cleavage by MIP of an octapeptide after initial
CC       processing by MPP is a required step for a subgroup of nuclear-encoded
CC       precursor proteins destined for the matrix or the inner membrane.
CC       Cleaves precursor proteins of respiratory components, including
CC       subunits of the electron transport chain and tricarboxylic acid cycle
CC       enzymes, and components of the mitochondrial genetic machinery,
CC       including ribosomal proteins, translation factors, and proteins
CC       required for mitochondrial DNA metabolism. {ECO:0000269|PubMed:7593000,
CC       ECO:0000269|PubMed:8035833}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Release of an N-terminal octapeptide as second stage of
CC         processing of some proteins imported into the mitochondrion.;
CC         EC=3.4.24.59;
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC       Note=Binds 1 zinc ion. {ECO:0000250};
CC   -!- ACTIVITY REGULATION: Stimulated by Fe(2+).
CC       {ECO:0000269|PubMed:10332043}.
CC   -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC       {ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:16823961,
CC       ECO:0000269|PubMed:8831696}.
CC   -!- MISCELLANEOUS: Present with 2690 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SIMILARITY: Belongs to the peptidase M3 family. {ECO:0000305}.
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DR   EMBL; U10243; AAA21278.1; -; Genomic_DNA.
DR   EMBL; Z28134; CAA81975.1; -; Genomic_DNA.
DR   EMBL; BK006944; DAA09028.2; -; Genomic_DNA.
DR   PIR; S37963; S37963.
DR   RefSeq; NP_012788.2; NM_001179700.2.
DR   AlphaFoldDB; P35999; -.
DR   SMR; P35999; -.
DR   BioGRID; 34002; 83.
DR   DIP; DIP-2670N; -.
DR   IntAct; P35999; 1.
DR   MINT; P35999; -.
DR   STRING; 4932.YKL134C; -.
DR   MEROPS; M03.006; -.
DR   MaxQB; P35999; -.
DR   PaxDb; P35999; -.
DR   PRIDE; P35999; -.
DR   EnsemblFungi; YKL134C_mRNA; YKL134C; YKL134C.
DR   GeneID; 853724; -.
DR   KEGG; sce:YKL134C; -.
DR   SGD; S000001617; OCT1.
DR   VEuPathDB; FungiDB:YKL134C; -.
DR   eggNOG; KOG2090; Eukaryota.
DR   GeneTree; ENSGT00950000183171; -.
DR   HOGENOM; CLU_001805_0_0_1; -.
DR   InParanoid; P35999; -.
DR   OMA; VVYCDLF; -.
DR   BioCyc; YEAST:YKL134C-MON; -.
DR   PRO; PR:P35999; -.
DR   Proteomes; UP000002311; Chromosome XI.
DR   RNAct; P35999; protein.
DR   GO; GO:0005759; C:mitochondrial matrix; IDA:SGD.
DR   GO; GO:0005739; C:mitochondrion; HDA:SGD.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0004222; F:metalloendopeptidase activity; IDA:SGD.
DR   GO; GO:0006879; P:cellular iron ion homeostasis; IMP:SGD.
DR   GO; GO:0006518; P:peptide metabolic process; IBA:GO_Central.
DR   GO; GO:0006627; P:protein processing involved in protein targeting to mitochondrion; IMP:SGD.
DR   GO; GO:0050821; P:protein stabilization; IMP:SGD.
DR   GO; GO:0006508; P:proteolysis; IBA:GO_Central.
DR   Gene3D; 1.10.1370.10; -; 1.
DR   Gene3D; 3.40.390.10; -; 1.
DR   InterPro; IPR024079; MetalloPept_cat_dom_sf.
DR   InterPro; IPR024077; Neurolysin/TOP_dom2.
DR   InterPro; IPR045090; Pept_M3A_M3B.
DR   InterPro; IPR001567; Pept_M3A_M3B_dom.
DR   PANTHER; PTHR11804; PTHR11804; 1.
DR   Pfam; PF01432; Peptidase_M3; 1.
DR   PROSITE; PS00142; ZINC_PROTEASE; 1.
PE   1: Evidence at protein level;
KW   Hydrolase; Metal-binding; Metalloprotease; Mitochondrion; Protease;
KW   Reference proteome; Transit peptide; Zinc.
FT   TRANSIT         1..37
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           38..772
FT                   /note="Mitochondrial intermediate peptidase"
FT                   /id="PRO_0000028583"
FT   ACT_SITE        559
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT   BINDING         558
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT   BINDING         562
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10095"
FT   BINDING         587
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000305"
FT   MUTAGEN         131
FT                   /note="C->S,V: Affects protein stability, but has no effect
FT                   on peptidase activity."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         557
FT                   /note="F->R: Affects protein stability."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         558
FT                   /note="H->R: Abolishes proteolytic activity."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         559
FT                   /note="E->D: Abolishes proteolytic activity."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         561
FT                   /note="G->L: Affects protein stability."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         562
FT                   /note="H->R: Abolishes proteolytic activity."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         565
FT                   /note="H->R: Temperature sensitive; abolishes proteolytic
FT                   activity for RIP1, but not for COX4."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         578
FT                   /note="G->L: Temperature sensitive; abolishes proteolytic
FT                   activity for RIP1, but not for COX4."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         581
FT                   /note="C->S,V: Affects protein stability, but has no effect
FT                   on peptidase activity."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         584
FT                   /note="D->E: No effect."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         587
FT                   /note="E->D: Abolishes proteolytic activity."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         589
FT                   /note="P->L: No effect."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         590
FT                   /note="S->Y: Affects protein stability."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   MUTAGEN         594
FT                   /note="E->D: No effect."
FT                   /evidence="ECO:0000269|PubMed:8831696"
FT   CONFLICT        343..350
FT                   /note="MAKNPKDV -> WQDRRC (in Ref. 2; CAA81975)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        694..702
FT                   /note="YGATYYSYL -> SGQLITATY (in Ref. 2; CAA81975)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   772 AA;  88183 MW;  1C19A0655FAAE7CA CRC64;
     MLRTIILKAG SNASIPSPSR QNKLLRFFAT AGAVSRTSPG SIKKIFDDNS YWRNINGQDA
     NNSKISQYLF KKNKTGLFKN PYLTSPDGLR KFSQVSLQQA QELLDKMRND FSESGKLTYI
     MNLDRLSDTL CRVIDLCEFI RSTHPDDAFV RAAQDCHEQM FEFMNVLNTD VSLCNILKSV
     LNNPEVSSKL SAEELKVGKI LLDDFEKSGI YMNPDVREKF IQLSQEISLV GQEFINHTDY
     PGSNSVKIPC KDLDNSKVST FLLKQLNKDV KGQNYKVPTF GYAAYALLKS CENEMVRKKL
     WTALHSCSDK QVKRLSHLIK LRAILANLMH KTSYAEYQLE GKMAKNPKDV QDFILTLMNN
     TIEKTANELK FIAELKAKDL KKPLTTNTDE ILKLVRPWDR DYYTGKYFQL NPSNSPNAKE
     ISYYFTLGNV IQGLSDLFQQ IYGIRLEPAI TDEGETWSPD VRRLNVISEE EGIIGIIYCD
     LFERNGKTSN PAHFTVCCSR QIYPSETDFS TIQVGENPDG TYFQLPVISL VCNFSPILIA
     SKKSLCFLQL SEVETLFHEM GHAMHSMLGR THMQNISGTR CATDFVELPS ILMEHFAKDI
     RILTKIGKHY GTGETIQADM LQRFMKSTNF LQNCETYSQA KMAMLDQSFH DEKIISDIDN
     FDVVENYQAL ERRLKVLVDD QSNWCGRFGH LFGYGATYYS YLFDRTIASK IWYALFEDDP
     YSRKNGDKFK KHLLKWGGLK DPWKCIADVL ECPMLEKGGS DAMEFIAQSH KS
 
 
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