P35999 (PMIP_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Mitochondrial intermediate peptidase
Short name=MIP
EC=3.4.24.59

Gene names

Name:	OCT1
Synonyms:	MIP1
Ordered Locus Names:	YKL134C

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	772 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	Cleaves proteins, imported into the mitochondrion, to their mature size. While most mitochondrial precursor proteins are processed to the mature form in one step by mitochondrial processing peptidase (MPP), the sequential cleavage by MIP of an octapeptide after initial processing by MPP is a required step for a subgroup of nuclear-encoded precursor proteins destined for the matrix or the inner membrane. Cleaves precursor proteins of respiratory components, including subunits of the electron transport chain and tricarboxylic acid cycle enzymes, and components of the mitochondrial genetic machinery, including ribosomal proteins, translation factors, and proteins required for mitochondrial DNA metabolism. Ref.1 Ref.4
Catalytic activity	Release of an N-terminal octapeptide as second stage of processing of some proteins imported into the mitochondrion.
Cofactor	Binds 1 zinc ion By similarity.
Enzyme regulation	Stimulated by Fe2+. Ref.6
Subcellular location	Mitochondrion matrix Ref.5 Ref.7 Ref.9.
Miscellaneous	Present with 2690 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the peptidase M3 family.

Ontologies

Keywords
Cellular component	Mitochondrion
Domain	Transit peptide
Ligand	Metal-binding Zinc
Molecular function	Hydrolase Metalloprotease Protease
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cellular iron ion homeostasis Inferred from mutant phenotype Ref.6. Source: SGD protein processing involved in protein targeting to mitochondrion Inferred from mutant phenotype Ref.1. Source: SGD proteolysis Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	mitochondrial matrix Inferred from electronic annotation. Source: UniProtKB-SubCell mitochondrion Inferred from direct assay Ref.9. Source: SGD
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW metalloendopeptidase activity Inferred from mutant phenotype Ref.5. Source: SGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 37	37	Mitochondrion Potential
	Chain	38 – 772	735	Mitochondrial intermediate peptidase		PRO_0000028583
Sites
	Active site	559	1	By similarity
	Metal binding	558	1	Zinc; catalytic By similarity
	Metal binding	562	1	Zinc; catalytic By similarity
	Metal binding	565	1	Zinc; catalytic By similarity
Experimental info
	Mutagenesis	131	1	C → S or V: Affects protein stability, but has no effect on peptidase activity. Ref.5
	Mutagenesis	557	1	F → R: Affects protein stability. Ref.5
	Mutagenesis	558	1	H → R: Abolishes proteolytic activity. Ref.5
	Mutagenesis	559	1	E → D: Abolishes proteolytic activity. Ref.5
	Mutagenesis	561	1	G → L: Affects protein stability. Ref.5
	Mutagenesis	562	1	H → R: Abolishes proteolytic activity. Ref.5
	Mutagenesis	565	1	H → R: Temperature sensitive; abolishes proteolytic activity for RIP1, but not for COX4. Ref.5
	Mutagenesis	578	1	G → L: Temperature sensitive; abolishes proteolytic activity for RIP1, but not for COX4. Ref.5
	Mutagenesis	581	1	C → S or V: Affects protein stability, but has no effect on peptidase activity. Ref.5
	Mutagenesis	584	1	D → E: No effect. Ref.5
	Mutagenesis	587	1	E → D: Abolishes proteolytic activity. Ref.5
	Mutagenesis	589	1	P → L: No effect. Ref.5
	Mutagenesis	590	1	S → Y: Affects protein stability. Ref.5
	Mutagenesis	594	1	E → D: No effect. Ref.5
	Sequence conflict	343 – 350	8	MAKNPKDV → WQDRRC in CAA81975. Ref.2
	Sequence conflict	694 – 702	9	YGATYYSYL → SGQLITATY in CAA81975. Ref.2

Sequences

	Sequence		Length	Mass (Da)
	P35999 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: 1C19A0655FAAE7CA	FASTA	772	88,183
	10 20 30 40 50 60 MLRTIILKAG SNASIPSPSR QNKLLRFFAT AGAVSRTSPG SIKKIFDDNS YWRNINGQDA 70 80 90 100 110 120 NNSKISQYLF KKNKTGLFKN PYLTSPDGLR KFSQVSLQQA QELLDKMRND FSESGKLTYI 130 140 150 160 170 180 MNLDRLSDTL CRVIDLCEFI RSTHPDDAFV RAAQDCHEQM FEFMNVLNTD VSLCNILKSV 190 200 210 220 230 240 LNNPEVSSKL SAEELKVGKI LLDDFEKSGI YMNPDVREKF IQLSQEISLV GQEFINHTDY 250 260 270 280 290 300 PGSNSVKIPC KDLDNSKVST FLLKQLNKDV KGQNYKVPTF GYAAYALLKS CENEMVRKKL 310 320 330 340 350 360 WTALHSCSDK QVKRLSHLIK LRAILANLMH KTSYAEYQLE GKMAKNPKDV QDFILTLMNN 370 380 390 400 410 420 TIEKTANELK FIAELKAKDL KKPLTTNTDE ILKLVRPWDR DYYTGKYFQL NPSNSPNAKE 430 440 450 460 470 480 ISYYFTLGNV IQGLSDLFQQ IYGIRLEPAI TDEGETWSPD VRRLNVISEE EGIIGIIYCD 490 500 510 520 530 540 LFERNGKTSN PAHFTVCCSR QIYPSETDFS TIQVGENPDG TYFQLPVISL VCNFSPILIA 550 560 570 580 590 600 SKKSLCFLQL SEVETLFHEM GHAMHSMLGR THMQNISGTR CATDFVELPS ILMEHFAKDI 610 620 630 640 650 660 RILTKIGKHY GTGETIQADM LQRFMKSTNF LQNCETYSQA KMAMLDQSFH DEKIISDIDN 670 680 690 700 710 720 FDVVENYQAL ERRLKVLVDD QSNWCGRFGH LFGYGATYYS YLFDRTIASK IWYALFEDDP 730 740 750 760 770 YSRKNGDKFK KHLLKWGGLK DPWKCIADVL ECPMLEKGGS DAMEFIAQSH KS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"MIP1, a new yeast gene homologous to the rat mitochondrial intermediate peptidase gene, is required for oxidative metabolism in Saccharomyces cerevisiae." Isaya G., Miklos D., Rollins R.A. Mol. Cell. Biol. 14:5603-5616(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"Complete DNA sequence of yeast chromosome XI." Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W. Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 343-350 AND 694-702. Strain: ATCC 204508 / S288c.
[4]	"Prediction and identification of new natural substrates of the yeast mitochondrial intermediate peptidase." Branda S.S., Isaya G. J. Biol. Chem. 270:27366-27373(1995) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[5]	"Mutations in a putative zinc-binding domain inactivate the mitochondrial intermediate peptidase." Chew A., Rollins R.A., Sakati W.R., Isaya G. Biochem. Biophys. Res. Commun. 226:822-829(1996) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYS-131; PHE-557; HIS-558; GLE-559; GLY-561; HIS-562; HIS-565; GLY-578; CYS-581; ASP-584; GLU-587; PRO-589; SER-590 AND GLU-594, SUBCELLULAR LOCATION.
[6]	"Mitochondrial intermediate peptidase and the yeast frataxin homolog together maintain mitochondrial iron homeostasis in Saccharomyces cerevisiae." Branda S.S., Yang Z.Y., Chew A., Isaya G. Hum. Mol. Genet. 8:1099-1110(1999) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME REGULATION.
[7]	"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].
[8]	"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].
[9]	"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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	U10243 Genomic DNA. Translation: AAA21278.1. Z28134 Genomic DNA. Translation: CAA81975.1. BK006944 Genomic DNA. Translation: DAA09028.2.
PIR	S37963.
RefSeq	NP_012788.2. NM_001179700.2.
3D structure databases
ProteinModelPortal	P35999.
SMR	P35999. Positions 120-759.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-2670N.
IntAct	P35999. 1 interaction.
MINT	MINT-497669.
STRING	4932.YKL134C.
Protein family/group databases
MEROPS	M03.006.
Proteomic databases
PaxDb	P35999.
PRIDE	P35999.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YKL134C; YKL134C; YKL134C.
GeneID	853724.
KEGG	sce:YKL134C.
Organism-specific databases
SGD	S000001617. OCT1.
Phylogenomic databases
eggNOG	COG0339.
GeneTree	ENSGT00550000075047.
HOGENOM	HOG000076521.
KO	K01410.
OMA	TQLQVFY.
OrthoDB	EOG4GJ2XS.
Gene expression databases
Genevestigator	P35999.
GermOnline	YKL134C. Saccharomyces cerevisiae.
Family and domain databases
Gene3D	1.10.1370.10. 2 hits. 1.20.1050.40. 1 hit. 3.40.390.10. 1 hit.
InterPro	IPR024079. MetalloPept_cat_dom. IPR024077. Neurolysin/TOP_dom2. IPR024080. Neurolysin/TOP_N. IPR001567. Pept_M3A_M3B. [Graphical view]
Pfam	PF01432. Peptidase_M3. 1 hit. [Graphical view]
PROSITE	PS00142. ZINC_PROTEASE. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	974752.

Entry information

Entry name

PMIP_YEAST

Accession

Primary (citable) accession number: P35999
Secondary accession number(s): D6VX62, P51980

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 1, 1994
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 116 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program