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Protein

Lon protease homolog, mitochondrial

Gene

PIM1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

ATP-dependent serine protease that mediates the selective degradation of misfolded, unassembled or oxidatively damaged polypeptides as well as certain short-lived regulatory proteins in the mitochondrial matrix. May also have a chaperone function in the assembly of inner membrane protein complexes. Participates in the regulation of mitochondrial gene expression and in the maintenance of the integrity of the mitochondrial genome. Binds to mitochondrial DNA in a site-specific manner. Endogenous substrates include ACO2, ILV1, ILV2, LSC1, LYS4 and several oxidized proteins.UniRule annotation8 Publications

Kineticsi

  1. KM=40 µM for ATP for ATPase activity1 Publication

    pH dependencei

    Optimum pH is 7.9.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei1015UniRule annotation1
    Active sitei1058UniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi632 – 639ATPUniRule annotation8

    GO - Molecular functioni

    GO - Biological processi

    • cellular response to oxidative stress Source: UniProtKB-HAMAP
    • chaperone-mediated protein complex assembly Source: SGD
    • misfolded or incompletely synthesized protein catabolic process Source: SGD
    • mitochondrial DNA metabolic process Source: AgBase
    • mitochondrial respiratory chain complex assembly Source: AgBase
    • mitochondrion organization Source: GO_Central
    • oxidation-dependent protein catabolic process Source: UniProtKB-HAMAP
    • protein folding Source: AgBase
    • regulation of mitochondrial DNA replication Source: UniProtKB-HAMAP
    • response to heat Source: AgBase
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Protease, Serine protease

    Keywords - Ligandi

    ATP-binding, DNA-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-28925-MONOMER.

    Protein family/group databases

    MEROPSiS16.010.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lon protease homolog, mitochondrialUniRule annotation (EC:3.4.21.-UniRule annotation)
    Gene namesi
    Name:PIM1UniRule annotation
    Synonyms:LON
    Ordered Locus Names:YBL022C
    ORF Names:YBL0440
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    Proteomesi
    • UP000002311 Componenti: Chromosome II

    Organism-specific databases

    EuPathDBiFungiDB:YBL022C.
    SGDiS000000118. PIM1.

    Subcellular locationi

    GO - Cellular componenti

    • mitochondrial matrix Source: SGD
    Complete GO annotation...

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi638K → N: Abolishes ATP-binding. 2 Publications1
    Mutagenesisi1015S → A: Abolishes peptidase activity. 2 Publications1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 37MitochondrionUniRule annotationAdd BLAST37
    PropeptideiPRO_000039576138 – 98Removed in mature form; by autocatalysisUniRule annotation2 PublicationsAdd BLAST61
    ChainiPRO_000002673399 – 1133Lon protease homolog, mitochondrialAdd BLAST1035

    Proteomic databases

    MaxQBiP36775.
    PRIDEiP36775.

    PTM databases

    iPTMnetiP36775.

    Interactioni

    Subunit structurei

    Homoheptamer. Organized in a ring with a central cavity. Oligomerization is independent of its proteolytic activity and the autocatalytic maturation of its subunits.UniRule annotation2 Publications

    Protein-protein interaction databases

    BioGridi32676. 72 interactors.
    DIPiDIP-6629N.
    IntActiP36775. 13 interactors.
    MINTiMINT-626645.

    Structurei

    3D structure databases

    ProteinModelPortaliP36775.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini182 – 478Lon N-terminalPROSITE-ProRule annotationAdd BLAST297
    Domaini923 – 1109Lon proteolyticPROSITE-ProRule annotationAdd BLAST187

    Sequence similaritiesi

    Belongs to the peptidase S16 family.UniRule annotation
    Contains 1 Lon N-terminal domain.PROSITE-ProRule annotation
    Contains 1 Lon proteolytic domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    GeneTreeiENSGT00530000063553.
    HOGENOMiHOG000261409.
    InParanoidiP36775.
    KOiK08675.
    OMAiNDWEELP.
    OrthoDBiEOG092C0S6Z.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.40.50.300. 1 hit.
    HAMAPiMF_03120. lonm_euk. 1 hit.
    InterProiIPR003593. AAA+_ATPase.
    IPR003959. ATPase_AAA_core.
    IPR004815. Lon_bac/euk-typ.
    IPR027065. Lon_Prtase.
    IPR003111. LON_substr-bd_dom.
    IPR027503. Lonm_euk.
    IPR027417. P-loop_NTPase.
    IPR008269. Pept_S16_C.
    IPR008268. Peptidase_S16_AS.
    IPR015947. PUA-like_domain.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
    [Graphical view]
    PANTHERiPTHR10046. PTHR10046. 2 hits.
    PfamiPF00004. AAA. 1 hit.
    PF05362. Lon_C. 1 hit.
    PF02190. LON_substr_bdg. 1 hit.
    [Graphical view]
    SMARTiSM00382. AAA. 1 hit.
    SM00464. LON. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    SSF54211. SSF54211. 1 hit.
    SSF88697. SSF88697. 1 hit.
    TIGRFAMsiTIGR00763. lon. 1 hit.
    PROSITEiPS51787. LON_N. 1 hit.
    PS51786. LON_PROTEOLYTIC. 1 hit.
    PS01046. LON_SER. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P36775-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLRTRTTKTL STVARTTRAI QYYRSIAKTA AVSQRRFAST LTVRDVENIK
    60 70 80 90 100
    PSHIIKSPTW QEFQHQLKDP RYMEHFAQLD AQFARHFMAT NSGKSILAKD
    110 120 130 140 150
    DSTSQKKDED VKIVPDEKDT DNDVEPTRDD EIVNKDQEGE ASKNSRSSAS
    160 170 180 190 200
    GGGQSSSSRS DSGDGSSKQK PPKDVPEVYP QMLALPIARR PLFPGFYKAV
    210 220 230 240 250
    VISDERVMKA IKEMLDRQQP YIGAFMLKNS EEDTDVITDK NDVYDVGVLA
    260 270 280 290 300
    QITSAFPSKD EKTGTETMTA LLYPHRRIKI DELFPPNEEK EKSKEQAKDT
    310 320 330 340 350
    DTETTVVEDA NNPEDQESTS PATPKLEDIV VERIPDSELQ HHKRVEATEE
    360 370 380 390 400
    ESEELDDIQE GEDINPTEFL KNYNVSLVNV LNLEDEPFDR KSPVINALTS
    410 420 430 440 450
    EILKVFKEIS QLNTMFREQI ATFSASIQSA TTNIFEEPAR LADFAAAVSA
    460 470 480 490 500
    GEEDELQDIL SSLNIEHRLE KSLLVLKKEL MNAELQNKIS KDVETKIQKR
    510 520 530 540 550
    QREYYLMEQL KGIKRELGID DGRDKLIDTY KERIKSLKLP DSVQKIFDDE
    560 570 580 590 600
    ITKLSTLETS MSEFGVIRNY LDWLTSIPWG KHSKEQYSIP RAKKILDEDH
    610 620 630 640 650
    YGMVDVKDRI LEFIAVGKLL GKVDGKIICF VGPPGVGKTS IGKSIARALN
    660 670 680 690 700
    RKFFRFSVGG MTDVAEIKGH RRTYIGALPG RVVQALKKCQ TQNPLILIDE
    710 720 730 740 750
    IDKIGHGGIH GDPSAALLEV LDPEQNNSFL DNYLDIPIDL SKVLFVCTAN
    760 770 780 790 800
    SLETIPRPLL DRMEVIELTG YVAEDKVKIA EQYLVPSAKK SAGLENSHVD
    810 820 830 840 850
    MTEDAITALM KYYCRESGVR NLKKHIEKIY RKAALQVVKK LSIEDSPTSS
    860 870 880 890 900
    ADSKPKESVS SEEKAENNAK SSSEKTKDNN SEKTSDDIEA LKTSEKINVS
    910 920 930 940 950
    ISQKNLKDYV GPPVYTTDRL YETTPPGVVM GLAWTNMGGC SLYVESVLEQ
    960 970 980 990 1000
    PLHNCKHPTF ERTGQLGDVM KESSRLAYSF AKMYLAQKFP ENRFFEKASI
    1010 1020 1030 1040 1050
    HLHCPEGATP KDGPSAGVTM ATSFLSLALN KSIDPTVAMT GELTLTGKVL
    1060 1070 1080 1090 1100
    RIGGLREKAV AAKRSGAKTI IFPKDNLNDW EELPDNVKEG LEPLAADWYN
    1110 1120 1130
    DIFQKLFKDV NTKEGNSVWK AEFEILDAKK EKD
    Length:1,133
    Mass (Da):127,112
    Last modified:October 1, 1994 - v2
    Checksum:i281CAB94579FFF09
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti509Q → R in AAA53625 (PubMed:8146662).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X74544 Genomic DNA. Translation: CAA52634.1.
    L28110 mRNA. Translation: AAA53625.1.
    Z35783 Genomic DNA. Translation: CAA84841.1.
    M20318 Genomic DNA. Translation: AAA53539.1.
    BK006936 Genomic DNA. Translation: DAA07098.1.
    PIRiS43938.
    RefSeqiNP_009531.1. NM_001178262.1.

    Genome annotation databases

    EnsemblFungiiYBL022C; YBL022C; YBL022C.
    GeneIDi852259.
    KEGGisce:YBL022C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X74544 Genomic DNA. Translation: CAA52634.1.
    L28110 mRNA. Translation: AAA53625.1.
    Z35783 Genomic DNA. Translation: CAA84841.1.
    M20318 Genomic DNA. Translation: AAA53539.1.
    BK006936 Genomic DNA. Translation: DAA07098.1.
    PIRiS43938.
    RefSeqiNP_009531.1. NM_001178262.1.

    3D structure databases

    ProteinModelPortaliP36775.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi32676. 72 interactors.
    DIPiDIP-6629N.
    IntActiP36775. 13 interactors.
    MINTiMINT-626645.

    Protein family/group databases

    MEROPSiS16.010.

    PTM databases

    iPTMnetiP36775.

    Proteomic databases

    MaxQBiP36775.
    PRIDEiP36775.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblFungiiYBL022C; YBL022C; YBL022C.
    GeneIDi852259.
    KEGGisce:YBL022C.

    Organism-specific databases

    EuPathDBiFungiDB:YBL022C.
    SGDiS000000118. PIM1.

    Phylogenomic databases

    GeneTreeiENSGT00530000063553.
    HOGENOMiHOG000261409.
    InParanoidiP36775.
    KOiK08675.
    OMAiNDWEELP.
    OrthoDBiEOG092C0S6Z.

    Enzyme and pathway databases

    BioCyciYEAST:G3O-28925-MONOMER.

    Miscellaneous databases

    PROiP36775.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.40.50.300. 1 hit.
    HAMAPiMF_03120. lonm_euk. 1 hit.
    InterProiIPR003593. AAA+_ATPase.
    IPR003959. ATPase_AAA_core.
    IPR004815. Lon_bac/euk-typ.
    IPR027065. Lon_Prtase.
    IPR003111. LON_substr-bd_dom.
    IPR027503. Lonm_euk.
    IPR027417. P-loop_NTPase.
    IPR008269. Pept_S16_C.
    IPR008268. Peptidase_S16_AS.
    IPR015947. PUA-like_domain.
    IPR020568. Ribosomal_S5_D2-typ_fold.
    IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
    [Graphical view]
    PANTHERiPTHR10046. PTHR10046. 2 hits.
    PfamiPF00004. AAA. 1 hit.
    PF05362. Lon_C. 1 hit.
    PF02190. LON_substr_bdg. 1 hit.
    [Graphical view]
    SMARTiSM00382. AAA. 1 hit.
    SM00464. LON. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.
    SSF54211. SSF54211. 1 hit.
    SSF88697. SSF88697. 1 hit.
    TIGRFAMsiTIGR00763. lon. 1 hit.
    PROSITEiPS51787. LON_N. 1 hit.
    PS51786. LON_PROTEOLYTIC. 1 hit.
    PS01046. LON_SER. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiLONM_YEAST
    AccessioniPrimary (citable) accession number: P36775
    Secondary accession number(s): D6VPX8, P13435
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: October 1, 1994
    Last modified: November 2, 2016
    This is version 152 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 14500 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Peptidase families
      Classification of peptidase families and list of entries
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome II
      Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.