MPPB_ARATH
ID MPPB_ARATH Reviewed; 531 AA.
AC Q42290; Q0WWT6; Q9SGA7;
DT 24-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 2.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=Probable mitochondrial-processing peptidase subunit beta, mitochondrial;
DE EC=3.4.24.64 {ECO:0000250|UniProtKB:P10507};
DE AltName: Full=Beta-MPP;
DE AltName: Full=Complex III subunit I;
DE AltName: Full=Core protein I;
DE AltName: Full=Cytochrome b-c1 complex subunit 1, mitochondrial;
DE AltName: Full=Ubiquinol-cytochrome c oxidoreductase core protein 1;
DE Flags: Precursor;
GN Name=MPPbeta; OrderedLocusNames=At3g02090 {ECO:0000312|Araport:AT3G02090};
GN ORFNames=F1C9.12 {ECO:0000312|EMBL:AAF14827.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130713; DOI=10.1038/35048706;
RA Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL Nature 408:820-822(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 70-531.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 321-421.
RC STRAIN=cv. Columbia; TISSUE=Leaf;
RX PubMed=8580968; DOI=10.1046/j.1365-313x.1996.09010101.x;
RA Cooke R., Raynal M., Laudie M., Grellet F., Delseny M., Morris P.-C.,
RA Guerrier D., Giraudat J., Quigley F., Clabault G., Li Y.-F., Mache R.,
RA Krivitzky M., Gy I.J.-J., Kreis M., Lecharny A., Parmentier Y., Marbach J.,
RA Fleck J., Clement B., Philipps G., Herve C., Bardet C., Tremousaygue D.,
RA Lescure B., Lacomme C., Roby D., Jourjon M.-F., Chabrier P.,
RA Charpenteau J.-L., Desprez T., Amselem J., Chiapello H., Hoefte H.;
RT "Further progress towards a catalogue of all Arabidopsis genes: analysis of
RT a set of 5000 non-redundant ESTs.";
RL Plant J. 9:101-124(1996).
RN [6]
RP SUBUNIT.
RX PubMed=12970493; DOI=10.1104/pp.103.024620;
RA Eubel H., Jansch L., Braun H.P.;
RT "New insights into the respiratory chain of plant mitochondria.
RT Supercomplexes and a unique composition of complex II.";
RL Plant Physiol. 133:274-286(2003).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND SUBCELLULAR LOCATION [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Landsberg erecta;
RX PubMed=14671022; DOI=10.1105/tpc.016055;
RA Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J.,
RA Millar A.H.;
RT "Experimental analysis of the Arabidopsis mitochondrial proteome highlights
RT signaling and regulatory components, provides assessment of targeting
RT prediction programs, and indicates plant-specific mitochondrial proteins.";
RL Plant Cell 16:241-256(2004).
RN [8]
RP SUBCELLULAR LOCATION, SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=18189341; DOI=10.1021/pr700595p;
RA Meyer E.H., Taylor N.L., Millar A.H.;
RT "Resolving and identifying protein components of plant mitochondrial
RT respiratory complexes using three dimensions of gel electrophoresis.";
RL J. Proteome Res. 7:786-794(2008).
RN [9]
RP SUBUNIT, IDENTIFICATION BY MASS SPECTROMETRY, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
RX PubMed=18305213; DOI=10.1104/pp.107.111260;
RA Zsigmond L., Rigo G., Szarka A., Szekely G., Oetvoes K., Darula Z.,
RA Medzihradszky K.F., Koncz C., Koncz Z., Szabados L.;
RT "Arabidopsis PPR40 connects abiotic stress responses to mitochondrial
RT electron transport.";
RL Plant Physiol. 146:1721-1737(2008).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY, AND CLEAVAGE OF TRANSIT PEPTIDE AFTER
RP TYR-78.
RX PubMed=25732537; DOI=10.1093/jxb/erv064;
RA Carrie C., Venne A.S., Zahedi R.P., Soll J.;
RT "Identification of cleavage sites and substrate proteins for two
RT mitochondrial intermediate peptidases in Arabidopsis thaliana.";
RL J. Exp. Bot. 66:2691-2708(2015).
CC -!- FUNCTION: Catalytic subunit of the essential mitochondrial processing
CC protease (MPP), which cleaves the mitochondrial sequence off newly
CC imported precursors proteins (By similarity). Preferentially, cleaves
CC after an arginine at position P2 (By similarity).
CC {ECO:0000250|UniProtKB:P10507, ECO:0000250|UniProtKB:Q03346}.
CC -!- FUNCTION: Component of the ubiquinol-cytochrome c oxidoreductase, a
CC multisubunit transmembrane complex that is part of the mitochondrial
CC electron transport chain which drives oxidative phosphorylation. The
CC respiratory chain contains 3 multisubunit complexes succinate
CC dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase
CC (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase
CC (complex IV, CIV), that cooperate to transfer electrons derived from
CC NADH and succinate to molecular oxygen, creating an electrochemical
CC gradient over the inner membrane that drives transmembrane transport
CC and the ATP synthase. The cytochrome b-c1 complex catalyzes electron
CC transfer from ubiquinol to cytochrome c, linking this redox reaction to
CC translocation of protons across the mitochondrial inner membrane, with
CC protons being carried across the membrane as hydrogens on the quinol.
CC In the process called Q cycle, 2 protons are consumed from the matrix,
CC 4 protons are released into the intermembrane space and 2 electrons are
CC passed to cytochrome c. {ECO:0000250|UniProtKB:P07256}.
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:0000250|UniProtKB:P10507};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P10507};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:P10507};
CC -!- ACTIVITY REGULATION: Binding to the alpha subunit is required for
CC catalytic activity. {ECO:0000250|UniProtKB:P10507}.
CC -!- SUBUNIT: Heterodimer of an alpha subunit and a beta subunit subunits,
CC forming the mitochondrial processing protease (MPP) in which the alpha
CC subunit is involved in substrate recognition and binding and the beta
CC subunit is the catalytic subunit (By similarity). Component of the
CC ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex
CC III, CIII), a multisubunit enzyme composed of 10 subunits. The complex
CC is composed of 3 respiratory subunits cytochrome b (MT-CYB), cytochrome
CC c1 (CYC1-1 or CYC1-2) and Rieske protein (UCR1-1 or UCR1-2), 2 core
CC protein subunits MPPalpha1 (or MPPalpha2) and MPPB, and 5 low-molecular
CC weight protein subunits QCR7-1 (or QCR7-2), UCRQ-1 (or UCRQ-2), QCR9,
CC UCRY and probably QCR6-1 (or QCR6-2) (PubMed:18189341,
CC PubMed:18305213). The complex exists as an obligatory dimer and forms
CC supercomplexes (SCs) in the inner mitochondrial membrane with NADH-
CC ubiquinone oxidoreductase (complex I, CI), resulting in different
CC assemblies (supercomplexes SCI(1)III(2) and SCI(2)III(4))
CC (PubMed:12970493). {ECO:0000250|UniProtKB:P10507,
CC ECO:0000269|PubMed:12970493, ECO:0000269|PubMed:18189341,
CC ECO:0000269|PubMed:18305213}.
CC -!- INTERACTION:
CC Q42290; Q9LDU5: TIFY11A; NbExp=3; IntAct=EBI-1777952, EBI-2312095;
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:14671022,
CC ECO:0000305|PubMed:25732537}. Mitochondrion inner membrane
CC {ECO:0000269|PubMed:18189341}; Peripheral membrane protein
CC {ECO:0000250|UniProtKB:P07256}; Matrix side
CC {ECO:0000250|UniProtKB:P07256}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q42290-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q42290-2; Sequence=VSP_018097;
CC -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing donor splice
CC site. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the peptidase M16 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; AC011664; AAF14827.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73761.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE73762.1; -; Genomic_DNA.
DR EMBL; AY126990; AAM83217.1; -; mRNA.
DR EMBL; BT000830; AAN33205.1; -; mRNA.
DR EMBL; BT000662; AAN31809.1; -; mRNA.
DR EMBL; BT001915; AAN71914.1; -; mRNA.
DR EMBL; AK226251; BAE98412.1; -; mRNA.
DR EMBL; Z35354; CAA84561.1; -; mRNA.
DR RefSeq; NP_186858.1; NM_111075.3. [Q42290-1]
DR RefSeq; NP_850500.1; NM_180169.1. [Q42290-2]
DR AlphaFoldDB; Q42290; -.
DR SMR; Q42290; -.
DR BioGRID; 6417; 8.
DR IntAct; Q42290; 5.
DR MINT; Q42290; -.
DR STRING; 3702.AT3G02090.2; -.
DR MEROPS; M16.003; -.
DR PaxDb; Q42290; -.
DR PRIDE; Q42290; -.
DR ProteomicsDB; 238277; -. [Q42290-1]
DR EnsemblPlants; AT3G02090.1; AT3G02090.1; AT3G02090. [Q42290-1]
DR EnsemblPlants; AT3G02090.2; AT3G02090.2; AT3G02090. [Q42290-2]
DR GeneID; 821084; -.
DR Gramene; AT3G02090.1; AT3G02090.1; AT3G02090. [Q42290-1]
DR Gramene; AT3G02090.2; AT3G02090.2; AT3G02090. [Q42290-2]
DR KEGG; ath:AT3G02090; -.
DR Araport; AT3G02090; -.
DR TAIR; locus:2078623; AT3G02090.
DR eggNOG; KOG0960; Eukaryota.
DR HOGENOM; CLU_009902_4_2_1; -.
DR InParanoid; Q42290; -.
DR OMA; IDVVCDM; -.
DR OrthoDB; 638125at2759; -.
DR PhylomeDB; Q42290; -.
DR BioCyc; ARA:AT3G02090-MON; -.
DR BioCyc; MetaCyc:AT3G02090-MON; -.
DR PRO; PR:Q42290; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q42290; baseline and differential.
DR Genevisible; Q42290; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0005743; C:mitochondrial inner membrane; HDA:TAIR.
DR GO; GO:0005758; C:mitochondrial intermembrane space; HDA:TAIR.
DR GO; GO:0005759; C:mitochondrial matrix; HDA:TAIR.
DR GO; GO:0005741; C:mitochondrial outer membrane; HDA:TAIR.
DR GO; GO:0005750; C:mitochondrial respiratory chain complex III; HDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; HDA:TAIR.
DR GO; GO:0005730; C:nucleolus; HDA:TAIR.
DR GO; GO:0009505; C:plant-type cell wall; HDA:TAIR.
DR GO; GO:0000325; C:plant-type vacuole; HDA:TAIR.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; HDA:TAIR.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
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 Alternative splicing; Hydrolase; Membrane; Metal-binding; Metalloprotease;
KW Mitochondrion; Mitochondrion inner membrane; Oxidoreductase; Protease;
KW Reference proteome; Transit peptide; Zinc.
FT TRANSIT 1..78
FT /note="Mitochondrion"
FT /evidence="ECO:0000269|PubMed:25732537"
FT CHAIN 79..531
FT /note="Probable mitochondrial-processing peptidase subunit
FT beta, mitochondrial"
FT /id="PRO_0000045852"
FT REGION 30..50
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 144
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10096"
FT ACT_SITE 214
FT /evidence="ECO:0000305"
FT BINDING 141
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10096"
FT BINDING 145
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10096"
FT BINDING 221
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000250|UniProtKB:P10507"
FT VAR_SEQ 504..531
FT /note="DIAISAIGPIQDLPDYNKFRRRTYWNRY -> VRHCNLSYWSNPRFARLQQI
FT QTQNLLEPVLRL (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_018097"
FT CONFLICT 132
FT /note="E -> G (in Ref. 4; BAE98412)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 531 AA; 59160 MW; 08A3953AD192E6B5 CRC64;
MAMKNLLSLA RRSQRRLFLT QATRSSSSFS AIDSVPASAS PTALSPPPPH LMPYDHAAEI
IKNKIKKLEN PDKRFLKYAS PHPILASHNH ILSAPETRVT TLPNGLRVAT ESNLSAKTAT
VGVWIDAGSR FESDETNGTA HFLEHMIFKG TDRRTVRALE EEIEDIGGHL NAYTSREQTT
YYAKVLDSNV NQALDVLADI LQNSKFEEQR INRERDVILR EMQEVEGQTD EVVLDHLHAT
AFQYTPLGRT ILGPAQNVKS ITREDLQNYI KTHYTASRMV IAAAGAVKHE EVVEQVKKLF
TKLSSDPTTT SQLVANEPAS FTGSEVRMID DDLPLAQFAV AFEGASWTDP DSVALMVMQT
MLGSWNKNVG GGKHVGSDLT QRVAINEIAE SIMAFNTNYK DTGLFGVYAV AKADCLDDLS
YAIMYEVTKL AYRVSDADVT RARNQLKSSL LLHMDGTSPI AEDIGRQLLT YGRRIPTAEL
FARIDAVDAS TVKRVANKYI YDKDIAISAI GPIQDLPDYN KFRRRTYWNR Y
