ICP55_YEAST
ID ICP55_YEAST Reviewed; 511 AA.
AC P40051; D3DLY4;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 174.
DE RecName: Full=Intermediate cleaving peptidase 55;
DE EC=3.4.11.26 {ECO:0000269|PubMed:19720832, ECO:0000269|PubMed:19837041};
DE AltName: Full=Intermediate cleaving peptidase of 55 kDa;
GN Name=ICP55; OrderedLocusNames=YER078C;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [4]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [5]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=16823961; DOI=10.1021/pr050477f;
RA Reinders J., Zahedi R.P., Pfanner N., Meisinger C., Sickmann A.;
RT "Toward the complete yeast mitochondrial proteome: multidimensional
RT separation techniques for mitochondrial proteomics.";
RL J. Proteome Res. 5:1543-1554(2006).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, FUNCTION, AND
RP CATALYTIC ACTIVITY.
RX PubMed=19837041; DOI=10.1016/j.cell.2009.07.045;
RA Vogtle F.N., Wortelkamp S., Zahedi R.P., Becker D., Leidhold C.,
RA Gevaert K., Kellermann J., Voos W., Sickmann A., Pfanner N., Meisinger C.;
RT "Global analysis of the mitochondrial N-proteome identifies a processing
RT peptidase critical for protein stability.";
RL Cell 139:428-439(2009).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBCELLULAR LOCATION.
RX PubMed=19720832; DOI=10.1074/jbc.m109.034694;
RA Naamati A., Regev-Rudzki N., Galperin S., Lill R., Pines O.;
RT "Dual targeting of Nfs1 and discovery of its novel processing enzyme,
RT Icp55.";
RL J. Biol. Chem. 284:30200-30208(2009).
CC -!- FUNCTION: Aminopeptidase which cleaves preprotein intermediates that
CC carry destabilizing N-ter amino acid residues after the mitochondrial
CC processing peptidase (MPP) cleavage site and is thus critical for
CC stabilization of the mitochondrial proteome.
CC {ECO:0000269|PubMed:19720832, ECO:0000269|PubMed:19837041}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=The enzyme cleaves the 36-Pro-Pro-37 bond of cysteine
CC desulfurase (EC 2.8.1.7) removing three amino acid residues (Tyr-Ser-
CC Pro) from the N-terminus after cleavage by mitochondrial processing
CC peptidase.; EC=3.4.11.26; Evidence={ECO:0000269|PubMed:19720832,
CC ECO:0000269|PubMed:19837041};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000305};
CC Note=Binds 2 manganese ions per subunit. {ECO:0000305};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19720832}.
CC Mitochondrion inner membrane {ECO:0000269|PubMed:16823961,
CC ECO:0000269|PubMed:19720832}; Peripheral membrane protein
CC {ECO:0000269|PubMed:19720832}; Matrix side
CC {ECO:0000269|PubMed:19720832}. Note=Has the same dual localization
CC (mitochondrion and nucleus) as one of its substrate, NFS1.
CC {ECO:0000269|PubMed:19720832}.
CC -!- MISCELLANEOUS: Present with 5080 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the peptidase M24B family. {ECO:0000305}.
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DR EMBL; U18839; AAB64633.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07738.1; -; Genomic_DNA.
DR PIR; S50581; S50581.
DR RefSeq; NP_011001.1; NM_001178969.1.
DR PDB; 6A9T; X-ray; 2.15 A; A=58-511.
DR PDB; 6A9U; X-ray; 2.40 A; A=58-511.
DR PDB; 6A9V; X-ray; 2.90 A; A=44-511.
DR PDBsum; 6A9T; -.
DR PDBsum; 6A9U; -.
DR PDBsum; 6A9V; -.
DR AlphaFoldDB; P40051; -.
DR SMR; P40051; -.
DR BioGRID; 36823; 120.
DR DIP; DIP-4941N; -.
DR IntAct; P40051; 4.
DR MINT; P40051; -.
DR STRING; 4932.YER078C; -.
DR MaxQB; P40051; -.
DR PaxDb; P40051; -.
DR PRIDE; P40051; -.
DR EnsemblFungi; YER078C_mRNA; YER078C; YER078C.
DR GeneID; 856811; -.
DR KEGG; sce:YER078C; -.
DR SGD; S000000880; ICP55.
DR VEuPathDB; FungiDB:YER078C; -.
DR eggNOG; KOG2414; Eukaryota.
DR GeneTree; ENSGT00940000153657; -.
DR HOGENOM; CLU_017266_1_1_1; -.
DR InParanoid; P40051; -.
DR OMA; GWADTEL; -.
DR BioCyc; MetaCyc:G3O-30249-MON; -.
DR BioCyc; YEAST:G3O-30249-MON; -.
DR BRENDA; 3.4.11.26; 984.
DR BRENDA; 3.4.11.9; 984.
DR PRO; PR:P40051; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40051; protein.
DR GO; GO:0031314; C:extrinsic component of mitochondrial inner membrane; IDA:SGD.
DR GO; GO:0005739; C:mitochondrion; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0004177; F:aminopeptidase activity; IDA:SGD.
DR GO; GO:0030145; F:manganese ion binding; IEA:InterPro.
DR GO; GO:0070006; F:metalloaminopeptidase activity; IEA:InterPro.
DR GO; GO:0008233; F:peptidase activity; IBA:GO_Central.
DR GO; GO:0016485; P:protein processing; IMP:SGD.
DR GO; GO:0050821; P:protein stabilization; IMP:SGD.
DR Gene3D; 3.40.350.10; -; 1.
DR Gene3D; 3.90.230.10; -; 1.
DR InterPro; IPR007865; Aminopep_P_N.
DR InterPro; IPR029149; Creatin/AminoP/Spt16_NTD.
DR InterPro; IPR036005; Creatinase/aminopeptidase-like.
DR InterPro; IPR000994; Pept_M24.
DR InterPro; IPR001131; Peptidase_M24B_aminopep-P_CS.
DR Pfam; PF05195; AMP_N; 1.
DR Pfam; PF00557; Peptidase_M24; 1.
DR SMART; SM01011; AMP_N; 1.
DR SUPFAM; SSF53092; SSF53092; 1.
DR SUPFAM; SSF55920; SSF55920; 1.
DR PROSITE; PS00491; PROLINE_PEPTIDASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aminopeptidase; Hydrolase; Manganese; Membrane;
KW Metal-binding; Metalloprotease; Mitochondrion;
KW Mitochondrion inner membrane; Nucleus; Protease; Reference proteome.
FT CHAIN 1..511
FT /note="Intermediate cleaving peptidase 55"
FT /id="PRO_0000185098"
FT BINDING 327
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 338
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 338
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 417
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 444
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 467
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 467
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 67..78
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 83..90
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 109..115
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 147..152
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 158..164
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 174..176
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 177..186
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 189..192
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 204..213
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:6A9U"
FT HELIX 235..242
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 247..268
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 275..289
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 292..296
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 299..302
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 303..307
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 322..327
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 330..332
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 340..344
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 351..369
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 373..375
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 379..396
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 407..410
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 420..424
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 440..443
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 446..449
FT /evidence="ECO:0007829|PDB:6A9T"
FT TURN 457..461
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 462..465
FT /evidence="ECO:0007829|PDB:6A9T"
FT STRAND 467..479
FT /evidence="ECO:0007829|PDB:6A9T"
FT TURN 480..483
FT /evidence="ECO:0007829|PDB:6A9T"
FT HELIX 488..497
FT /evidence="ECO:0007829|PDB:6A9T"
SQ SEQUENCE 511 AA; 57990 MW; B62FB0D0C53B5F2F CRC64;
MLHRINPVRF SMQSCQRYFS KLVSPLEQHK SNTFTNRVRI PIEAGQPLHE TRPFLIKSGE
LTPGISALEY YERRIRLAET LPPKSCVILA GNDIQFASGA VFYPFQQEND LFYLSGWNEP
NSVMILEKPT DSLSDTIFHM LVPPKDAFAE KWEGFRSGVY GVQEIFNADE SASINDLSKY
LPKIINRNDF IYFDMLSTSN PSSSNFKHIK SLLDGSGNSN RSLNSIANKT IKPISKRIAE
FRKIKSPQEL RIMRRAGQIS GRSFNQAFAK RFRNERTLDS FLHYKFISGG CDKDAYIPVV
ATGSNSLCIH YTRNDDVMFD DEMVLVDAAG SLGGYCADIS RTWPNSGKFT DAQRDLYEAV
LNVQRDCIKL CKASNNYSLH DIHEKSITLM KQELKNLGID KVSGWNVEKL YPHYIGHNLG
LDVHDVPKVS RYEPLKVGQV ITIEPGLYIP NEESFPSYFR NVGIRIEDDI AIGEDTYTNL
TVEAVKEIDD LENVMQNGLS TKFEEDQVAP L
