P36775 (LONM_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Lon protease homolog, mitochondrial
EC=3.4.21.-

Gene names

Name:	PIM1
Synonyms:	LON
Ordered Locus Names:	YBL022C
ORF Names:	YBL0440

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	1133 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.1 Ref.2 Ref.7 Ref.8 Ref.9 Ref.10 Ref.15 Ref.17
Subunit structure	Homoheptamer. Organized in a ring with a central cavity. Oligomerization is independent of its proteolytic activity and the autocatalytic maturation of its subunits. Ref.8 Ref.12
Subcellular location	Mitochondrion matrix Ref.7 Ref.13 Ref.16.
Miscellaneous	Present with 14500 molecules/cell in log phase SD medium. HAMAP-Rule MF_03120
Sequence similarities	Belongs to the peptidase S16 family. Contains 1 Lon domain.
Biophysicochemical properties	Kinetic parameters: KM=40 µM for ATP for ATPase activity Ref.9 pH dependence: Optimum pH is 7.9.

Ontologies

Keywords
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Hydrolase Protease Serine protease
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	cellular response to oxidative stress Inferred from Biological aspect of Ancestor. Source: RefGenome chaperone-mediated protein complex assembly Inferred from genetic interaction Ref.10. Source: SGD misfolded or incompletely synthesized protein catabolic process Inferred from mutant phenotype PubMed 16336126PubMed 7957078. Source: SGD mitochondrion organization Inferred from Biological aspect of Ancestor. Source: RefGenome oxidation-dependent protein catabolic process Inferred from Biological aspect of Ancestor. Source: RefGenome protein homooligomerization Inferred from Biological aspect of Ancestor. Source: RefGenome response to hypoxia Inferred from Biological aspect of Ancestor. Source: RefGenome
Cellular_component	mitochondrial nucleoid Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	ATP binding Inferred from Biological aspect of Ancestor. Source: RefGenome ATP-dependent peptidase activity Inferred from mutant phenotype Ref.2Ref.1. Source: SGD mitochondrial light strand promoter anti-sense binding Inferred from Biological aspect of Ancestor. Source: RefGenome serine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro single-stranded DNA binding Inferred from Biological aspect of Ancestor. Source: RefGenome single-stranded RNA binding Inferred from Biological aspect of Ancestor. Source: RefGenome
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
DBP5	P20449	1	EBI-10179,EBI-5617

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 37	37	Mitochondrion Potential
	Propeptide	38 – 98	61	Removed in mature form; by autocatalysis HAMAP-Rule MF_03120		PRO_0000395761
	Chain	99 – 1133	1035	Lon protease homolog, mitochondrial HAMAP-Rule MF_03120		PRO_0000026733
Regions
	Domain	183 – 478	296	Lon
	Nucleotide binding	632 – 639	8	ATP By similarity
Sites
	Active site	1015	1	By similarity
	Active site	1058	1	By similarity
Experimental info
	Mutagenesis	638	1	K → N: Abolishes ATP-binding. Ref.7 Ref.10
	Mutagenesis	1015	1	S → A: Abolishes peptidase activity. Ref.7 Ref.10
	Sequence conflict	509	1	Q → R in AAA53625. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P36775 [UniParc]. Last modified October 1, 1994. Version 2. Checksum: 281CAB94579FFF09	FASTA	1,133	127,112
	10 20 30 40 50 60 MLRTRTTKTL STVARTTRAI QYYRSIAKTA AVSQRRFAST LTVRDVENIK PSHIIKSPTW 70 80 90 100 110 120 QEFQHQLKDP RYMEHFAQLD AQFARHFMAT NSGKSILAKD DSTSQKKDED VKIVPDEKDT 130 140 150 160 170 180 DNDVEPTRDD EIVNKDQEGE ASKNSRSSAS GGGQSSSSRS DSGDGSSKQK PPKDVPEVYP 190 200 210 220 230 240 QMLALPIARR PLFPGFYKAV VISDERVMKA IKEMLDRQQP YIGAFMLKNS EEDTDVITDK 250 260 270 280 290 300 NDVYDVGVLA QITSAFPSKD EKTGTETMTA LLYPHRRIKI DELFPPNEEK EKSKEQAKDT 310 320 330 340 350 360 DTETTVVEDA NNPEDQESTS PATPKLEDIV VERIPDSELQ HHKRVEATEE ESEELDDIQE 370 380 390 400 410 420 GEDINPTEFL KNYNVSLVNV LNLEDEPFDR KSPVINALTS EILKVFKEIS QLNTMFREQI 430 440 450 460 470 480 ATFSASIQSA TTNIFEEPAR LADFAAAVSA GEEDELQDIL SSLNIEHRLE KSLLVLKKEL 490 500 510 520 530 540 MNAELQNKIS KDVETKIQKR QREYYLMEQL KGIKRELGID DGRDKLIDTY KERIKSLKLP 550 560 570 580 590 600 DSVQKIFDDE ITKLSTLETS MSEFGVIRNY LDWLTSIPWG KHSKEQYSIP RAKKILDEDH 610 620 630 640 650 660 YGMVDVKDRI LEFIAVGKLL GKVDGKIICF VGPPGVGKTS IGKSIARALN RKFFRFSVGG 670 680 690 700 710 720 MTDVAEIKGH RRTYIGALPG RVVQALKKCQ TQNPLILIDE IDKIGHGGIH GDPSAALLEV 730 740 750 760 770 780 LDPEQNNSFL DNYLDIPIDL SKVLFVCTAN SLETIPRPLL DRMEVIELTG YVAEDKVKIA 790 800 810 820 830 840 EQYLVPSAKK SAGLENSHVD MTEDAITALM KYYCRESGVR NLKKHIEKIY RKAALQVVKK 850 860 870 880 890 900 LSIEDSPTSS ADSKPKESVS SEEKAENNAK SSSEKTKDNN SEKTSDDIEA LKTSEKINVS 910 920 930 940 950 960 ISQKNLKDYV GPPVYTTDRL YETTPPGVVM GLAWTNMGGC SLYVESVLEQ PLHNCKHPTF 970 980 990 1000 1010 1020 ERTGQLGDVM KESSRLAYSF AKMYLAQKFP ENRFFEKASI HLHCPEGATP KDGPSAGVTM 1030 1040 1050 1060 1070 1080 ATSFLSLALN KSIDPTVAMT GELTLTGKVL RIGGLREKAV AAKRSGAKTI IFPKDNLNDW 1090 1100 1110 1120 1130 EELPDNVKEG LEPLAADWYN DIFQKLFKDV NTKEGNSVWK AEFEILDAKK EKD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"PIM1 encodes a mitochondrial ATP-dependent protease that is required for mitochondrial function in the yeast Saccharomyces cerevisiae." van Dyck L., Pearce D.A., Sherman F. J. Biol. Chem. 269:238-242(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION. Strain: ATCC 204508 / S288c.
[2]	"Requirement for the yeast gene LON in intramitochondrial proteolysis and maintenance of respiration." Suzuki C.K., Suda K., Wang N., Schatz G. Science 264:273-276(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
[3]	Erratum Suzuki C.K., Suda K., Wang N., Schatz G. Science 264:891-891(1994) [PubMed] [Europe PMC] [Abstract]
[4]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"The HAP3 regulatory locus of Saccharomyces cerevisiae encodes divergent overlapping transcripts." Hahn S., Pinkham J., Wei R., Miller R., Guarente L. Mol. Cell. Biol. 8:655-663(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-216. Strain: ATCC MYA-3516 / BWG1-7A.
[7]	"Autocatalytic processing of the ATP-dependent PIM1 protease: crucial function of a pro-region for sorting to mitochondria." Wagner I., van Dyck L., Savel'ev A.S., Neupert W., Langer T. EMBO J. 16:7317-7325(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF N-TERMINUS, FUNCTION, MUTAGENESIS OF LYS-638 AND SER-1015, AUTOCATALYTIC PROCESSING, SUBCELLULAR LOCATION.
[8]	"The ATPase and protease domains of yeast mitochondrial Lon: roles in proteolysis and respiration-dependent growth." van Dijl J.M., Kutejova E., Suda K., Perecko D., Schatz G., Suzuki C.K. Proc. Natl. Acad. Sci. U.S.A. 95:10584-10589(1998) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF N-TERMINUS, FUNCTION, SUBUNIT.
[9]	"Yeast mitochondrial ATP-dependent protease: purification and comparison with the homologous rat enzyme and the bacterial ATP-dependent protease La." Kutejova E., Durcova G., Surovkova E., Kuzela S. FEBS Lett. 329:47-50(1993) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES.
[10]	"Promotion of mitochondrial membrane complex assembly by a proteolytically inactive yeast Lon." Rep M., van Dijl J.M., Suda K., Schatz G., Grivell L.A., Suzuki C.K. Science 274:103-106(1996) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF LYS-638 AND SER-1015.
[11]	Erratum Rep M., van Dijl J.M., Suda K., Schatz G., Grivell L.A., Suzuki C.K. Science 275:741-741(1997)
[12]	"Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits." Stahlberg H., Kutejova E., Suda K., Wolpensinger B., Lustig A., Schatz G., Engel A., Suzuki C.K. Proc. Natl. Acad. Sci. U.S.A. 96:6787-6790(1999) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[13]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[14]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[15]	"Cleavage site selection within a folded substrate by the ATP-dependent lon protease." Ondrovicova G., Liu T., Singh K., Tian B., Li H., Gakh O., Perecko D., Janata J., Granot Z., Orly J., Kutejova E., Suzuki C.K. J. Biol. Chem. 280:25103-25110(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[16]	"Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics." Reinders J., Zahedi R.P., Pfanner N., Meisinger C., Sickmann A. J. Proteome Res. 5:1543-1554(2006) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[17]	"Proteomic analysis of mitochondrial protein turnover: identification of novel substrate proteins of the matrix protease pim1." Major T., von Janowsky B., Ruppert T., Mogk A., Voos W. Mol. Cell. Biol. 26:762-776(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBSTRATE.
[18]	"Identification of novel oxidized protein substrates and physiological partners of the mitochondrial ATP-dependent Lon-like protease Pim1." Bayot A., Gareil M., Rogowska-Wrzesinska A., Roepstorff P., Friguet B., Bulteau A.L. J. Biol. Chem. 285:11445-11457(2010) [PubMed] [Europe PMC] [Abstract] Cited for: SUBSTRATE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
PIR	S43938.
RefSeq	NP_009531.1. NM_001178262.1.
3D structure databases
ProteinModelPortal	P36775.
SMR	P36775. Positions 391-518, 527-1109.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6629N.
IntAct	P36775. 16 interactions.
MINT	MINT-626645.
Protein family/group databases
MEROPS	S16.002.
Proteomic databases
PaxDb	P36775.
PeptideAtlas	P36775.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YBL022C; YBL022C; YBL022C.
GeneID	852259.
KEGG	sce:YBL022C.
Organism-specific databases
CYGD	YBL022c.
SGD	S000000118. PIM1.
Phylogenomic databases
eggNOG	COG0466.
GeneTree	ENSGT00530000063553.
HOGENOM	HOG000261409.
KO	K08675.
OMA	LKDYVGP.
OrthoDB	EOG4V46GS.
Gene expression databases
Genevestigator	P36775.
GermOnline	YBL022C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	3.30.230.10. 1 hit.
HAMAP	MF_03120. lonm_euk.
InterPro	IPR003593. AAA+_ATPase. IPR003959. ATPase_AAA_core. IPR027065. Lon_Prtase. IPR008269. Pept_S16_C. IPR004815. Pept_S16_lon. IPR003111. Pept_S16_N. IPR008268. Peptidase_S16_AS. IPR015947. PUA-like_domain. IPR020568. Ribosomal_S5_D2-typ_fold. IPR014721. Ribosomal_S5_D2-typ_fold_subgr. [Graphical view]
PANTHER	PTHR10046. PTHR10046. 1 hit.
Pfam	PF00004. AAA. 1 hit. PF02190. LON. 1 hit. PF05362. Lon_C. 1 hit. [Graphical view]
SMART	SM00382. AAA. 1 hit. SM00464. LON. 1 hit. [Graphical view]
SUPFAM	SSF88697. PUA-like. 1 hit. SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.
TIGRFAMs	TIGR00763. lon. 1 hit.
PROSITE	PS01046. LON_SER. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	970847.

Entry information

Entry name

LONM_YEAST

Accession

Primary (citable) accession number: P36775
Secondary accession number(s): D6VPX8, P13435

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	October 1, 1994
Last modified:	May 1, 2013
This is version 120 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program