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Protein

Lon protease

Gene

lon

Organism
Escherichia coli (strain K12)
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 mutant and abnormal proteins as well as certain short-lived regulatory proteins, including some antitoxins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner. Endogenous substrates include the regulatory proteins RcsA and SulA, the transcriptional activator SoxS, UmuD and antitoxins CcdA, HipB and MazE (PubMed:8022284, PubMed:16460757, PubMed:22720069, PubMed:24375411). Its overproduction specifically inhibits translation through at least two different pathways, one of them being the YoeB-YefM toxin-antitoxin system (PubMed:15009896).8 Publications

Catalytic activityi

Hydrolysis of proteins in presence of ATP.UniRule annotation

Enzyme regulationi

Contains an allosteric site (distinct from its active site), whose occupancy by an unfolded polypeptide leads to enzyme activation.

Kineticsi

  1. KM=0.201 mM for ATP for ATPase activity1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei6791
    Active sitei722UniRule annotation1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi356 – 363ATPUniRule annotation8

    GO - Molecular functioni

    • ATPase activity Source: EcoliWiki
    • ATP binding Source: EcoCyc
    • ATP-dependent peptidase activity Source: EcoliWiki
    • DNA binding Source: EcoliWiki
    • peptidase activity Source: EcoliWiki
    • sequence-specific DNA binding Source: UniProtKB-HAMAP
    • serine-type endopeptidase activity Source: EcoliWiki

    GO - Biological processi

    • cellular response to stress Source: UniProtKB-HAMAP
    • misfolded or incompletely synthesized protein catabolic process Source: EcoCyc
    • proteolysis Source: EcoliWiki
    • response to heat Source: EcoliWiki
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Protease, Serine protease

    Keywords - Biological processi

    Stress response

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10542-MONOMER.
    ECOL316407:JW0429-MONOMER.
    MetaCyc:EG10542-MONOMER.
    BRENDAi3.4.21.53. 2026.

    Protein family/group databases

    MEROPSiS16.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lon proteaseUniRule annotation (EC:3.4.21.53UniRule annotation)
    Alternative name(s):
    ATP-dependent protease LaUniRule annotation
    Gene namesi
    Name:lonUniRule annotation
    Synonyms:capR, deg, lopA, muc
    Ordered Locus Names:b0439, JW0429
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10542. lon.

    Subcellular locationi

    GO - Cellular componenti

    • cytoplasm Source: EcoliWiki
    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    When both lon and ycgE are disrupted levels of OmpF decrease, leading to lower drug susceptibility, with a greater effect at 26 degrees than at 37 degrees Celsius. The mechanism is not yet understood (PubMed:19721064). Decreased persister cell formation upon antibiotic challenge due probably due to increased levels of MazF toxin (PubMed:24375411).2 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi362K → A: Loss of proteolytic activity and ATP-binding. 1 Publication1
    Mutagenesisi665H → Y: Loss of proteolytic activity. 1 Publication1
    Mutagenesisi667H → Y: Loss of proteolytic activity. 1 Publication1
    Mutagenesisi676D → N: Loss of proteolytic activity. 1 Publication1
    Mutagenesisi679S → A: Loss of proteolytic activity. 1 Publication1
    Mutagenesisi743D → N: No effect. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemovedUniRule annotation1 Publication
    ChainiPRO_00000761332 – 784Lon proteaseAdd BLAST783

    Proteomic databases

    PaxDbiP0A9M0.
    PRIDEiP0A9M0.

    Expressioni

    Inductioni

    By accumulation of abnormal proteins, such as at high temperatures. Under stress conditions.

    Interactioni

    Subunit structurei

    Homohexamer. Organized in a ring with a central cavity. ATP binding and hydrolysis do not affect the oligomeric state of the enzyme.UniRule annotation1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    torAP332252EBI-547203,EBI-557008

    Protein-protein interaction databases

    BioGridi4260734. 24 interactors.
    DIPiDIP-35845N.
    IntActiP0A9M0. 69 interactors.
    MINTiMINT-1224190.
    STRINGi511145.b0439.

    Structurei

    Secondary structure

    1784
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi9 – 18Combined sources10
    Beta strandi26 – 31Combined sources6
    Helixi34 – 44Combined sources11
    Turni45 – 47Combined sources3
    Beta strandi48 – 55Combined sources8
    Helixi65 – 67Combined sources3
    Beta strandi70 – 82Combined sources13
    Beta strandi88 – 105Combined sources18
    Beta strandi107 – 116Combined sources10
    Helixi124 – 145Combined sources22
    Helixi150 – 155Combined sources6
    Helixi162 – 171Combined sources10
    Helixi177 – 185Combined sources9
    Helixi189 – 242Combined sources54
    Helixi495 – 504Combined sources10
    Helixi506 – 513Combined sources8
    Turni518 – 520Combined sources3
    Beta strandi521 – 523Combined sources3
    Helixi525 – 535Combined sources11
    Beta strandi539 – 541Combined sources3
    Helixi542 – 560Combined sources19
    Beta strandi568 – 570Combined sources3
    Turni572 – 574Combined sources3
    Helixi575 – 579Combined sources5
    Beta strandi596 – 604Combined sources9
    Beta strandi607 – 619Combined sources13
    Beta strandi624 – 630Combined sources7
    Helixi632 – 647Combined sources16
    Helixi649 – 652Combined sources4
    Turni656 – 660Combined sources5
    Beta strandi661 – 667Combined sources7
    Beta strandi675 – 678Combined sources4
    Helixi681 – 693Combined sources13
    Beta strandi701 – 703Combined sources3
    Beta strandi712 – 714Combined sources3
    Helixi719 – 728Combined sources10
    Beta strandi733 – 737Combined sources5
    Helixi738 – 746Combined sources9
    Helixi749 – 754Combined sources6
    Beta strandi755 – 762Combined sources8
    Helixi763 – 770Combined sources8
    Beta strandi771 – 773Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1QZMX-ray1.90A491-584[»]
    1RR9X-ray2.10A/B/C/D/E/F585-784[»]
    1RREX-ray1.75A/B/C/D/E/F585-784[»]
    2ANEX-ray2.03A/B/C/D/E/F/G/H1-118[»]
    3LJCX-ray2.60A1-245[»]
    ProteinModelPortaliP0A9M0.
    SMRiP0A9M0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A9M0.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini11 – 202Lon N-terminalPROSITE-ProRule annotationAdd BLAST192
    Domaini592 – 773Lon proteolyticPROSITE-ProRule annotationAdd BLAST182

    Compositional bias

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Compositional biasi211 – 219Arg/Lys-rich (basic)9
    Compositional biasi240 – 252Asp/Glu-rich (acidic)Add BLAST13
    Compositional biasi255 – 270Arg/Lys-rich (basic)Add BLAST16

    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

    Phylogenomic databases

    eggNOGiENOG4105C6P. Bacteria.
    COG0466. LUCA.
    HOGENOMiHOG000261408.
    InParanoidiP0A9M0.
    KOiK01338.
    OMAiDRMDILR.
    PhylomeDBiP0A9M0.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.40.50.300. 1 hit.
    HAMAPiMF_01973. lon_bact. 1 hit.
    InterProiIPR003593. AAA+_ATPase.
    IPR003959. ATPase_AAA_core.
    IPR027543. Lon_bac.
    IPR004815. Lon_bac/euk-typ.
    IPR027065. Lon_Prtase.
    IPR003111. LON_substr-bd_dom.
    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. 1 hit.
    PfamiPF00004. AAA. 1 hit.
    PF05362. Lon_C. 1 hit.
    PF02190. LON_substr_bdg. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001174. Lon_proteas. 1 hit.
    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.

    P0A9M0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNPERSERIE IPVLPLRDVV VYPHMVIPLF VGREKSIRCL EAAMDHDKKI
    60 70 80 90 100
    MLVAQKEAST DEPGVNDLFT VGTVASILQM LKLPDGTVKV LVEGLQRARI
    110 120 130 140 150
    SALSDNGEHF SAKAEYLESP TIDEREQEVL VRTAISQFEG YIKLNKKIPP
    160 170 180 190 200
    EVLTSLNSID DPARLADTIA AHMPLKLADK QSVLEMSDVN ERLEYLMAMM
    210 220 230 240 250
    ESEIDLLQVE KRIRNRVKKQ MEKSQREYYL NEQMKAIQKE LGEMDDAPDE
    260 270 280 290 300
    NEALKRKIDA AKMPKEAKEK AEAELQKLKM MSPMSAEATV VRGYIDWMVQ
    310 320 330 340 350
    VPWNARSKVK KDLRQAQEIL DTDHYGLERV KDRILEYLAV QSRVNKIKGP
    360 370 380 390 400
    ILCLVGPPGV GKTSLGQSIA KATGRKYVRM ALGGVRDEAE IRGHRRTYIG
    410 420 430 440 450
    SMPGKLIQKM AKVGVKNPLF LLDEIDKMSS DMRGDPASAL LEVLDPEQNV
    460 470 480 490 500
    AFSDHYLEVD YDLSDVMFVA TSNSMNIPAP LLDRMEVIRL SGYTEDEKLN
    510 520 530 540 550
    IAKRHLLPKQ IERNALKKGE LTVDDSAIIG IIRYYTREAG VRGLEREISK
    560 570 580 590 600
    LCRKAVKQLL LDKSLKHIEI NGDNLHDYLG VQRFDYGRAD NENRVGQVTG
    610 620 630 640 650
    LAWTEVGGDL LTIETACVPG KGKLTYTGSL GEVMQESIQA ALTVVRARAE
    660 670 680 690 700
    KLGINPDFYE KRDIHVHVPE GATPKDGPSA GIAMCTALVS CLTGNPVRAD
    710 720 730 740 750
    VAMTGEITLR GQVLPIGGLK EKLLAAHRGG IKTVLIPFEN KRDLEEIPDN
    760 770 780
    VIADLDIHPV KRIEEVLTLA LQNEPSGMQV VTAK
    Length:784
    Mass (Da):87,438
    Last modified:July 19, 2005 - v1
    Checksum:i4042499C97694EF8
    GO

    Sequence cautioni

    The sequence AAA23537 differs from that shown. Reason: Frameshift at position 16.Curated
    The sequence AAB40195 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti264 – 317PKEAK…LRQAQ → RKRQKRKRTGVAEAENDVSD VGRSDRSAWLYRLDGTGAVE CAYEGQKRPASGA in AAA24078 (PubMed:3042779).CuratedAdd BLAST54
    Sequence conflicti273A → R in AAA16837 (PubMed:8226758).Curated1
    Sequence conflicti307S → T in AAA16837 (PubMed:8226758).Curated1
    Sequence conflicti539 – 563AGVRG…LLLDK → RACVVWSVKSPNCVAKRLSS YCSIT in AAA24078 (PubMed:3042779).CuratedAdd BLAST25
    Sequence conflicti772Q → R in AAA16837 (PubMed:8226758).Curated1
    Sequence conflicti779 – 784QVVTAK → HHSLRRRCSTASTYYWAKS in AAA24079 (PubMed:3289547).Curated6

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L12349 Unassigned DNA. Translation: AAC36871.1.
    M38347 Genomic DNA. Translation: AAA24079.1.
    L20572 Unassigned DNA. Translation: AAA16837.1.
    J03896 Genomic DNA. Translation: AAA24078.1.
    U82664 Genomic DNA. Translation: AAB40195.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73542.1.
    AP009048 Genomic DNA. Translation: BAE76219.1.
    M10153 Genomic DNA. Translation: AAA23537.1. Frameshift.
    PIRiA23101.
    G64773. SUECLA.
    RefSeqiNP_414973.1. NC_000913.3.
    WP_001295325.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73542; AAC73542; b0439.
    BAE76219; BAE76219; BAE76219.
    GeneIDi945085.
    KEGGiecj:JW0429.
    eco:b0439.
    PATRICi32116031. VBIEscCol129921_0457.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L12349 Unassigned DNA. Translation: AAC36871.1.
    M38347 Genomic DNA. Translation: AAA24079.1.
    L20572 Unassigned DNA. Translation: AAA16837.1.
    J03896 Genomic DNA. Translation: AAA24078.1.
    U82664 Genomic DNA. Translation: AAB40195.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73542.1.
    AP009048 Genomic DNA. Translation: BAE76219.1.
    M10153 Genomic DNA. Translation: AAA23537.1. Frameshift.
    PIRiA23101.
    G64773. SUECLA.
    RefSeqiNP_414973.1. NC_000913.3.
    WP_001295325.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1QZMX-ray1.90A491-584[»]
    1RR9X-ray2.10A/B/C/D/E/F585-784[»]
    1RREX-ray1.75A/B/C/D/E/F585-784[»]
    2ANEX-ray2.03A/B/C/D/E/F/G/H1-118[»]
    3LJCX-ray2.60A1-245[»]
    ProteinModelPortaliP0A9M0.
    SMRiP0A9M0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260734. 24 interactors.
    DIPiDIP-35845N.
    IntActiP0A9M0. 69 interactors.
    MINTiMINT-1224190.
    STRINGi511145.b0439.

    Protein family/group databases

    MEROPSiS16.001.

    Proteomic databases

    PaxDbiP0A9M0.
    PRIDEiP0A9M0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73542; AAC73542; b0439.
    BAE76219; BAE76219; BAE76219.
    GeneIDi945085.
    KEGGiecj:JW0429.
    eco:b0439.
    PATRICi32116031. VBIEscCol129921_0457.

    Organism-specific databases

    EchoBASEiEB0537.
    EcoGeneiEG10542. lon.

    Phylogenomic databases

    eggNOGiENOG4105C6P. Bacteria.
    COG0466. LUCA.
    HOGENOMiHOG000261408.
    InParanoidiP0A9M0.
    KOiK01338.
    OMAiDRMDILR.
    PhylomeDBiP0A9M0.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10542-MONOMER.
    ECOL316407:JW0429-MONOMER.
    MetaCyc:EG10542-MONOMER.
    BRENDAi3.4.21.53. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0A9M0.
    PROiP0A9M0.

    Family and domain databases

    Gene3Di3.30.230.10. 1 hit.
    3.40.50.300. 1 hit.
    HAMAPiMF_01973. lon_bact. 1 hit.
    InterProiIPR003593. AAA+_ATPase.
    IPR003959. ATPase_AAA_core.
    IPR027543. Lon_bac.
    IPR004815. Lon_bac/euk-typ.
    IPR027065. Lon_Prtase.
    IPR003111. LON_substr-bd_dom.
    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. 1 hit.
    PfamiPF00004. AAA. 1 hit.
    PF05362. Lon_C. 1 hit.
    PF02190. LON_substr_bdg. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001174. Lon_proteas. 1 hit.
    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 nameiLON_ECOLI
    AccessioniPrimary (citable) accession number: P0A9M0
    Secondary accession number(s): P08177, P78219, Q2MBY7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: July 19, 2005
    Last modified: November 2, 2016
    This is version 111 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Both its proteolytic and protein-activated ATPase activities are stimulated by DNA, especially single-stranded DNA.
    Both high- and low-affinity ATPase sites are present in the homooligomer. Optimal peptidase activity requires ATP binding and hydrolysis at both sites, but ATP hydrolysis is not stoichiometrically linked to peptide hydrolysis.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Peptidase families
      Classification of peptidase families and list of entries
    4. SIMILARITY comments
      Index of protein domains and families

    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.