MPPB_YEAST
ID MPPB_YEAST Reviewed; 462 AA.
AC P10507; D6VYG9;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 1.
DT 03-AUG-2022, entry version 209.
DE RecName: Full=Mitochondrial-processing peptidase subunit beta {ECO:0000303|PubMed:9299349};
DE EC=3.4.24.64 {ECO:0000269|PubMed:2007593, ECO:0000269|PubMed:9299349, ECO:0000269|PubMed:9654444};
DE AltName: Full=Beta-MPP;
DE AltName: Full=Mitochondrial assembly protein 1 {ECO:0000303|PubMed:3044780};
DE AltName: Full=Processing enhancing protein {ECO:0000303|PubMed:3061797};
DE Short=PEP;
DE Flags: Precursor;
GN Name=MAS1 {ECO:0000303|PubMed:3044780};
GN Synonyms=MIF1 {ECO:0000303|PubMed:3061797};
GN OrderedLocusNames=YLR163C {ECO:0000312|SGD:S000004153}; ORFNames=L9632.10;
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 SUBCELLULAR LOCATION.
RX PubMed=3044780; DOI=10.1002/j.1460-2075.1988.tb02961.x;
RA Witte C., Jensen R.E., Yaffe M.P., Schatz G.;
RT "MAS1, a gene essential for yeast mitochondrial assembly, encodes a subunit
RT of the mitochondrial processing protease.";
RL EMBO J. 7:1439-1447(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169871;
RA Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W.,
RA Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A.,
RA Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K.,
RA Heuss-Neitzel D., Hilbert H., Hilger F., Kleine K., Koetter P., Louis E.J.,
RA Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S.,
RA Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D.,
RA Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M.,
RA Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P.,
RA Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M.,
RA Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K.,
RA Zollner A., Hani J., Hoheisel J.D.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII.";
RL Nature 387:87-90(1997).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP PROTEIN SEQUENCE OF 21-32, FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=2007593; DOI=10.1016/s0021-9258(18)38134-1;
RA Yang M., Geli V., Oppliger W., Suda K., James P., Schatz G.;
RT "The MAS-encoded processing protease of yeast mitochondria. Interaction of
RT the purified enzyme with signal peptides and a purified precursor
RT protein.";
RL J. Biol. Chem. 266:6416-6423(1991).
RN [6]
RP FUNCTION.
RX PubMed=3061797; DOI=10.1002/j.1460-2075.1988.tb03225.x;
RA Pollock R.A., Hartl F.-U., Cheng M.Y., Ostermann J., Horwich A.,
RA Neupert W.;
RT "The processing peptidase of yeast mitochondria: the two co-operating
RT components MPP and PEP are structurally related.";
RL EMBO J. 7:3493-3500(1988).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, INTERACTION WITH MAS2,
RP AND MUTAGENESIS OF GLU-89; SER-133; TYR-198; LYS-234; PRO-249; THR-301;
RP SER-333; LYS-364 AND ARG-400.
RX PubMed=9299349; DOI=10.1006/jmbi.1997.1231;
RA Luciano P., Geoffroy S., Brandt A., Hernandez J.F., Geli V.;
RT "Functional cooperation of the mitochondrial processing peptidase
RT subunits.";
RL J. Mol. Biol. 272:213-225(1997).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, AND
RP MUTAGENESIS OF HIS-70.
RX PubMed=9654444; DOI=10.1006/jmbi.1998.1858;
RA Luciano P., Tokatlidis K., Chambre I., Germanique J.C., Geli V.;
RT "The mitochondrial processing peptidase behaves as a zinc-
RT metallopeptidase.";
RL J. Mol. Biol. 280:193-199(1998).
RN [9]
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 [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-243, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 21-462 IN COMPLEX WITH MAS2; ZINC
RP AND SUBSTRATES, AND ACTIVE SITE.
RX PubMed=11470436; DOI=10.1016/s0969-2126(01)00621-9;
RA Taylor A.B., Smith B.S., Kitada S., Kojima K., Miyaura H., Otwinowski Z.,
RA Ito A., Deisenhofer J.;
RT "Crystal structures of mitochondrial processing peptidase reveal the mode
RT for specific cleavage of import signal sequences.";
RL Structure 9:615-625(2001).
CC -!- FUNCTION: Catalytic subunit of the essential mitochondrial processing
CC protease (MPP), which cleaves the mitochondrial sequence off newly
CC imported precursors proteins (PubMed:2007593, PubMed:9299349,
CC PubMed:9654444). Preferentially, cleaves after an arginine at position
CC P2 (By similarity). {ECO:0000250|UniProtKB:Q03346,
CC ECO:0000269|PubMed:2007593, ECO:0000269|PubMed:9299349,
CC ECO:0000269|PubMed:9654444}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Release of N-terminal transit peptides from precursor proteins
CC imported into the mitochondrion, typically with Arg in position P2.;
CC EC=3.4.24.64; Evidence={ECO:0000269|PubMed:2007593,
CC ECO:0000269|PubMed:9299349, ECO:0000269|PubMed:9654444};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:9654444};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:11470436,
CC ECO:0000269|PubMed:9654444};
CC -!- ACTIVITY REGULATION: Binding to MAS2 is required for catalytic activity
CC (PubMed:9654444, PubMed:9299349). Inhibited by high levels (> 1uM) of
CC zinc (PubMed:9654444). Inhibited by metal chelators
CC ethylenediaminetetraacetic acid (EDTA) and O-phenanthroline
CC (PubMed:9654444). {ECO:0000269|PubMed:9299349,
CC ECO:0000269|PubMed:9654444}.
CC -!- SUBUNIT: Heterodimer of MAS2 (alpha) and MAS1 (beta) subunits, forming
CC the mitochondrial processing protease (MPP) in which MAS2 is involved
CC in substrate recognition and binding and MAS1 is the catalytic subunit.
CC {ECO:0000269|PubMed:11470436, ECO:0000269|PubMed:9299349}.
CC -!- INTERACTION:
CC P10507; P11914: MAS2; NbExp=4; IntAct=EBI-11212, EBI-11205;
CC -!- SUBCELLULAR LOCATION: Mitochondrion matrix
CC {ECO:0000269|PubMed:3044780}.
CC -!- MISCELLANEOUS: Present with 1360 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the peptidase M16 family. {ECO:0000305}.
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DR EMBL; X07649; CAA30489.1; -; Genomic_DNA.
DR EMBL; U51921; AAB67487.1; -; Genomic_DNA.
DR EMBL; AY693198; AAT93217.1; -; Genomic_DNA.
DR EMBL; BK006945; DAA09485.1; -; Genomic_DNA.
DR PIR; S00552; S00552.
DR RefSeq; NP_013264.1; NM_001182050.1.
DR PDB; 1HR6; X-ray; 2.50 A; B/D/F/H=21-462.
DR PDB; 1HR7; X-ray; 2.55 A; B/D/F/H=21-462.
DR PDB; 1HR8; X-ray; 2.70 A; B/D/F/H=21-462.
DR PDB; 1HR9; X-ray; 3.01 A; B/D/F/H=21-462.
DR PDBsum; 1HR6; -.
DR PDBsum; 1HR7; -.
DR PDBsum; 1HR8; -.
DR PDBsum; 1HR9; -.
DR AlphaFoldDB; P10507; -.
DR SMR; P10507; -.
DR BioGRID; 31436; 94.
DR ComplexPortal; CPX-1630; Mitochondrial processing peptidase complex.
DR DIP; DIP-2402N; -.
DR IntAct; P10507; 16.
DR MINT; P10507; -.
DR STRING; 4932.YLR163C; -.
DR MEROPS; M16.003; -.
DR MEROPS; M16.980; -.
DR iPTMnet; P10507; -.
DR MaxQB; P10507; -.
DR PaxDb; P10507; -.
DR PRIDE; P10507; -.
DR EnsemblFungi; YLR163C_mRNA; YLR163C; YLR163C.
DR GeneID; 850860; -.
DR KEGG; sce:YLR163C; -.
DR SGD; S000004153; MAS1.
DR VEuPathDB; FungiDB:YLR163C; -.
DR eggNOG; KOG0960; Eukaryota.
DR GeneTree; ENSGT00940000156608; -.
DR HOGENOM; CLU_009902_4_0_1; -.
DR InParanoid; P10507; -.
DR OMA; IDVVCDM; -.
DR BioCyc; MetaCyc:G3O-32293-MON; -.
DR BioCyc; YEAST:G3O-32293-MON; -.
DR BRENDA; 3.4.24.64; 984.
DR Reactome; R-SCE-611105; Respiratory electron transport.
DR SABIO-RK; P10507; -.
DR EvolutionaryTrace; P10507; -.
DR PRO; PR:P10507; -.
DR Proteomes; UP000002311; Chromosome XII.
DR RNAct; P10507; protein.
DR GO; GO:0005759; C:mitochondrial matrix; TAS:Reactome.
DR GO; GO:0017087; C:mitochondrial processing peptidase complex; IDA:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; IDA:ComplexPortal.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004222; F:metalloendopeptidase activity; IDA:UniProtKB.
DR GO; GO:0006627; P:protein processing involved in protein targeting to mitochondrion; IDA:SGD.
DR InterPro; IPR011249; Metalloenz_LuxS/M16.
DR InterPro; IPR011765; Pept_M16_N.
DR InterPro; IPR001431; Pept_M16_Zn_BS.
DR InterPro; IPR007863; Peptidase_M16_C.
DR Pfam; PF00675; Peptidase_M16; 1.
DR Pfam; PF05193; Peptidase_M16_C; 1.
DR SUPFAM; SSF63411; SSF63411; 2.
DR PROSITE; PS00143; INSULINASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Metal-binding;
KW Metalloprotease; Mitochondrion; Phosphoprotein; Protease;
KW Reference proteome; Transit peptide; Zinc.
FT TRANSIT 1..20
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:2007593"
FT CHAIN 21..462
FT /note="Mitochondrial-processing peptidase subunit beta"
FT /id="PRO_0000026784"
FT ACT_SITE 73
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:11470436,
FT ECO:0007744|PDB:1HR6"
FT BINDING 70
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10096,
FT ECO:0000269|PubMed:11470436, ECO:0000269|PubMed:9654444,
FT ECO:0007744|PDB:1HR6, ECO:0007744|PDB:1HR7,
FT ECO:0007744|PDB:1HR8, ECO:0007744|PDB:1HR9"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10096,
FT ECO:0000269|PubMed:11470436, ECO:0007744|PDB:1HR6,
FT ECO:0007744|PDB:1HR7, ECO:0007744|PDB:1HR8,
FT ECO:0007744|PDB:1HR9"
FT BINDING 150
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10096,
FT ECO:0000269|PubMed:11470436, ECO:0007744|PDB:1HR6,
FT ECO:0007744|PDB:1HR7, ECO:0007744|PDB:1HR8,
FT ECO:0007744|PDB:1HR9"
FT MOD_RES 243
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MUTAGEN 70
FT /note="H->R: Loss of zinc binding. Loss of catalytic
FT activity."
FT /evidence="ECO:0000269|PubMed:9654444"
FT MUTAGEN 89
FT /note="E->A: Loss of catalytic activity and loss of binding
FT to MAS2."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 133
FT /note="S->A: Loss of catalytic activity. No effect on the
FT binding to MAS2."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 198
FT /note="Y->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 234
FT /note="K->A: Loss of catalytic activity and loss of binding
FT to MAS2."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 249
FT /note="P->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 301
FT /note="T->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 333
FT /note="S->A: Loss of catalytic activity. No effect on the
FT binding to MAS2."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 364
FT /note="K->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:9299349"
FT MUTAGEN 400
FT /note="R->A: No effect on catalytic activity."
FT /evidence="ECO:0000269|PubMed:9299349"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 36..41
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 46..55
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:1HR6"
FT TURN 63..67
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 68..75
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 85..94
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 105..115
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 119..131
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 137..154
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 158..170
FT /evidence="ECO:0007829|PDB:1HR6"
FT TURN 171..173
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 175..177
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 184..189
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 192..202
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 205..207
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 208..215
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 218..229
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 254..259
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 264..273
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 282..292
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 294..296
FT /evidence="ECO:0007829|PDB:1HR6"
FT TURN 297..299
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 302..305
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 308..314
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 321..329
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 334..343
FT /evidence="ECO:0007829|PDB:1HR6"
FT TURN 344..346
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 349..364
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 370..385
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 391..405
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 411..419
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 423..433
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 434..436
FT /evidence="ECO:0007829|PDB:1HR6"
FT STRAND 439..445
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 447..449
FT /evidence="ECO:0007829|PDB:1HR6"
FT HELIX 453..461
FT /evidence="ECO:0007829|PDB:1HR6"
SQ SEQUENCE 462 AA; 51084 MW; 084CE63C495EDFC4 CRC64;
MFSRTASKFR NTRRLLSTIS SQIPGTRTSK LPNGLTIATE YIPNTSSATV GIFVDAGSRA
ENVKNNGTAH FLEHLAFKGT QNRSQQGIEL EIENIGSHLN AYTSRENTVY YAKSLQEDIP
KAVDILSDIL TKSVLDNSAI ERERDVIIRE SEEVDKMYDE VVFDHLHEIT YKDQPLGRTI
LGPIKNIKSI TRTDLKDYIT KNYKGDRMVL AGAGAVDHEK LVQYAQKYFG HVPKSESPVP
LGSPRGPLPV FCRGERFIKE NTLPTTHIAI ALEGVSWSAP DYFVALATQA IVGNWDRAIG
TGTNSPSPLA VAASQNGSLA NSYMSFSTSY ADSGLWGMYI VTDSNEHNVQ LIVNEILKEW
KRIKSGKISD AEVNRAKAQL KAALLLSLDG STAIVEDIGR QVVTTGKRLS PEEVFEQVDK
ITKDDIIMWA NYRLQNKPVS MVALGNTSTV PNVSYIEEKL NQ
