ID   LONM_ORYSJ              Reviewed;        1002 AA.
AC   Q69UZ3; C7J5E5;
DT   13-JUL-2010, integrated into UniProtKB/Swiss-Prot.
DT   13-SEP-2004, sequence version 1.
DT   03-AUG-2022, entry version 112.
DE   RecName: Full=Lon protease homolog, mitochondrial {ECO:0000255|HAMAP-Rule:MF_03120};
DE            EC=3.4.21.53 {ECO:0000255|HAMAP-Rule:MF_03120};
GN   OrderedLocusNames=Os07g0689300, LOC_Os07g48960;
GN   ORFNames=OJ1165_F02.125, P0597G07.108;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 531-1002 (ISOFORM 1).
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
CC   -!- FUNCTION: ATP-dependent serine protease that mediates the selective
CC       degradation of misfolded, unassembled or oxidatively damaged
CC       polypeptides as well as certain short-lived regulatory proteins in the
CC       mitochondrial matrix. May also have a chaperone function in the
CC       assembly of inner membrane protein complexes. Participates in the
CC       regulation of mitochondrial gene expression and in the maintenance of
CC       the integrity of the mitochondrial genome. Binds to mitochondrial DNA
CC       in a site-specific manner. {ECO:0000255|HAMAP-Rule:MF_03120}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Hydrolysis of proteins in presence of ATP.; EC=3.4.21.53;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_03120};
CC   -!- SUBUNIT: Homohexamer or homoheptamer. Organized in a ring with a
CC       central cavity. {ECO:0000255|HAMAP-Rule:MF_03120}.
CC   -!- SUBCELLULAR LOCATION: Mitochondrion matrix {ECO:0000255|HAMAP-
CC       Rule:MF_03120}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q69UZ3-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q69UZ3-2; Sequence=VSP_039541;
CC   -!- MISCELLANEOUS: This protein may be expected to contain an N-terminal
CC       transit peptide but none has been predicted. {ECO:0000255|HAMAP-
CC       Rule:MF_03120}.
CC   -!- SIMILARITY: Belongs to the peptidase S16 family. {ECO:0000255|HAMAP-
CC       Rule:MF_03120}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AK068511; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
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DR   EMBL; AP003816; BAD30304.1; -; Genomic_DNA.
DR   EMBL; AP004316; BAD30597.1; -; Genomic_DNA.
DR   EMBL; AP008213; BAH94072.1; -; Genomic_DNA.
DR   EMBL; AP014963; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AK068511; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015647418.1; XM_015791932.1. [Q69UZ3-1]
DR   AlphaFoldDB; Q69UZ3; -.
DR   SMR; Q69UZ3; -.
DR   STRING; 4530.OS07T0689300-01; -.
DR   PaxDb; Q69UZ3; -.
DR   PRIDE; Q69UZ3; -.
DR   GeneID; 9270304; -.
DR   KEGG; osa:9270304; -.
DR   eggNOG; KOG2004; Eukaryota.
DR   HOGENOM; CLU_004109_0_1_1; -.
DR   InParanoid; Q69UZ3; -.
DR   OrthoDB; 528132at2759; -.
DR   Proteomes; UP000000763; Chromosome 7.
DR   Proteomes; UP000059680; Chromosome 7.
DR   Genevisible; Q69UZ3; OS.
DR   GO; GO:0005759; C:mitochondrial matrix; IBA:GO_Central.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0016887; F:ATP hydrolysis activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0004176; F:ATP-dependent peptidase activity; IBA:GO_Central.
DR   GO; GO:0043565; F:sequence-specific DNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0004252; F:serine-type endopeptidase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0003697; F:single-stranded DNA binding; IBA:GO_Central.
DR   GO; GO:0034599; P:cellular response to oxidative stress; IEA:UniProtKB-UniRule.
DR   GO; GO:0051131; P:chaperone-mediated protein complex assembly; IBA:GO_Central.
DR   GO; GO:0007005; P:mitochondrion organization; IBA:GO_Central.
DR   GO; GO:0070407; P:oxidation-dependent protein catabolic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0006515; P:protein quality control for misfolded or incompletely synthesized proteins; IBA:GO_Central.
DR   Gene3D; 2.30.130.40; -; 1.
DR   Gene3D; 3.30.230.10; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   HAMAP; MF_03120; lonm_euk; 1.
DR   InterPro; IPR003593; AAA+_ATPase.
DR   InterPro; IPR003959; ATPase_AAA_core.
DR   InterPro; IPR004815; Lon_bac/euk-typ.
DR   InterPro; IPR008269; Lon_proteolytic.
DR   InterPro; IPR027065; Lon_Prtase.
DR   InterPro; IPR003111; Lon_prtase_N.
DR   InterPro; IPR046336; Lon_prtase_N_sf.
DR   InterPro; IPR027503; Lonm_euk.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR008268; Peptidase_S16_AS.
DR   InterPro; IPR015947; PUA-like_sf.
DR   InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR   InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR   PANTHER; PTHR43718; PTHR43718; 1.
DR   Pfam; PF00004; AAA; 1.
DR   Pfam; PF05362; Lon_C; 1.
DR   Pfam; PF02190; LON_substr_bdg; 1.
DR   SMART; SM00382; AAA; 1.
DR   SMART; SM00464; LON; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   SUPFAM; SSF54211; SSF54211; 1.
DR   SUPFAM; SSF88697; SSF88697; 1.
DR   TIGRFAMs; TIGR00763; lon; 1.
DR   PROSITE; PS51787; LON_N; 1.
DR   PROSITE; PS51786; LON_PROTEOLYTIC; 1.
DR   PROSITE; PS01046; LON_SER; 1.
PE   2: Evidence at transcript level;
KW   Alternative splicing; ATP-binding; DNA-binding; Hydrolase; Mitochondrion;
KW   Nucleotide-binding; Protease; Reference proteome; Serine protease.
FT   CHAIN           1..1002
FT                   /note="Lon protease homolog, mitochondrial"
FT                   /id="PRO_0000395767"
FT   DOMAIN          102..311
FT                   /note="Lon N-terminal"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01123"
FT   DOMAIN          811..995
FT                   /note="Lon proteolytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01122"
FT   ACT_SITE        901
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03120"
FT   ACT_SITE        944
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03120"
FT   BINDING         468..475
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_03120"
FT   VAR_SEQ         742..767
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_039541"
SQ   SEQUENCE   1002 AA;  109543 MW;  EC55E8F74C41451F CRC64;
     MLRAAAAAAA VFPSRFAAAP AVAAVEEVRS PLLRVLGALR GGRVSTLGRR ARFCSNSAGS
     DSEAAAAEAK AEDAVAAEGE ADGKASSAIV PTVLRPEDCL SVIALPLPHR PLFPGFYMPI
     YVKDQKLLQA LVENRKRSIP YAGAFLVKDE EGTDPNIVTS SDSDKSIDDL KGKELLQRLN
     EVGTLAQITS IQGDQVVLLG HRRLKITEMV QEDPLTVKVD HLKEKPYDKD DDVIKATSFE
     VISTLREVLK ASSLWKDHVQ TYTQHMGDFN YPRLADFGAA ISGANKFLCQ EVLEELDVYK
     RLKLTLELVK KEMEISKLQQ SIAKAIEEKI SGDQRRYLLN EQLKAIKKEL GLETDDKTAL
     SAKFRERIEA KKEKCPAHVL QVIEEELTKL QLLEASSSEF NVTRNYLDWL TVLPWGNYSD
     ENFDVHHAQQ ILDEDHYGLS DVKERILEFI AVGKLRGTSQ GKIICLSGPP GVGKTSIGRS
     IARALNRKFY RFSVGGLADV AEIKGHRRTY VGAMPGKMVQ CLKSVGTANP LVLIDEIDKL
     GRGHSGDPAS ALLELLDPEQ NVNFLDHYLD VPIDLSKVLF VCTANVIEMI PNPLLDRMEI
     IAIAGYITDE KMHIARDYLE KNTREACGIK PEQAEVTDAA LLALIESYCR EAGVRNLQKQ
     IEKIYRKIAL QLVRQGVSNE PTQEAAIVTA SEEPNGGDSA NKLKDETMED PATENAAMTN
     ADTASKEASE LDLLNRTVDH DVHPAETPKE AVLTDSALST DKLCTPEGNK DMEGAKEESA
     DKAVEKVVID SSNLGDYVGK PVFQAERIYE QTPVGVVMGL AWTAMGGSTL YIETTKVEEG
     DGKGALVMTG QLGDVMKESA QIAHTVGRAI LLDKEPENLF FANSKVHLHV PAGSTPKDGP
     SAGCTMITSM LSLAMGKPVK KDLAMTGEVT LTGRILPIGG VKEKTIAARR SAVKTIVFPA
     ANKRDFDELA PNVKEGLEVH FVDTYNEIFD IAFQSETQTE TS