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Enzyme Nomenclature
Information on EC 3.4.11.26 - intermediate cleaving peptidase 55
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EC Tree
3.4.11.26 intermediate cleaving peptidase 55Specify your search results
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
The enzyme cleaves the Pro36-Pro37 bond of cysteine desulfurase (EC 2.8.1.7) removing three amino acid residues (Tyr-Ser-Pro) from the N-terminus after cleavage by mitochondrial processing peptidase.
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Icp55
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
The enzyme cleaves the Pro36-Pro37 bond of cysteine desulfurase (EC 2.8.1.7) removing three amino acid residues (Tyr-Ser-Pro) from the N-terminus after cleavage by mitochondrial processing peptidase.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
FSTPSDLDSELTR + H2O
STPSDLDSELTR + Phe
N-terminal peptide of protein Oxa1
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-
?
FTSEAAADGGQDQILSR + H2O
TSEAAADGGQDQILSR + Phe
N-terminal peptide of mitochondrial acyl carrier protein 3
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-
?
Isa2 + H2O
?
-
-
substrate is likely processed by isoform Icp55 in two consecutive steps, in which Icp55 removes two destabilizing amino acids: first Phe and then in a second round of processing Tyr, resulting in the mature stable protein
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?
SSLPSEAVDEK + H2O
SLPSEAVDEK + Ser
N-terminal peptide of protein At4g37930
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-
?
Tyr-Ser-Pro-Nfs1 + H2O
Nfs1 + Tyr-Ser-Pro
the enzyme is involved in the processing pathway of yeast Nfs1 during its translocation into the mitochondrial matrix. Nfs1 from Saccharomyces cerevisiae undergoes two steps of proteolytic processing: first the mitochondrial processing peptidase (MPP) cleaves the precursor between Phe33 and Tyr34. Then Icp55 cleaves between Pro36 and Pro37 removing three amino acids residues (Tyr-Ser-Pro)
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-
?
Tyr-Ser-Pro-Nfs1 + H2O
Nfs1 + Tyr-Ser-Pro
the enzyme is involved in the processing pathway of yeast Nfs1 during its translocation into the mitochondrial matrix. Nfs1 from Saccharomyces cerevisiae undergoes two steps of proteolytic processing: first the mitochondrial processing peptidase (MPP) cleaves the precursor between Phe33 and Tyr34. Then Icp55 cleaves between Pro36 and Pro37 removing three amino acids residues (Tyr-Ser-Pro). In the absence of Nfs1 processing by mitochondrial processing peptidase (MPP), the Nfs1 precursor is not cleaved by Icp55. The two prolines are of importance for the Icp55 cleavage reaction, because the replacement of a single proline changes the specificity to a new cleavage site without eliminating the cleavage reaction per se
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?
additional information
?
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enzyme is able to remove N-terminal amino acids L, Y, I, F, C, M of mitochondrial proteins
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?
additional information
?
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Icp55 is critical for stabilization of the mitochondrial proteome. Icp55 removes an amino acid from a characteristic set of N-termini of preprotein intermediates generated by mitochondrial processing peptidase. Thereby Icp55 converts instable intermediates into stable proteins
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?
additional information
?
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global analysis of the N-proteome of yeast mitochondria, revealing the N-termini of 615 different proteins. The N-proteome of icp55DELTA mitochondria yielded proteins whose N-terminus differs by one residue from the mature N-terminus of wild-type mitochondria. Icp55 cleaves between the last amino acid of the presequence (tyrosine, leucine or phenylalanine) and the first residue of the mature protein, preferentially serine, alanine and threonine. The most frequent residue tyrosine is efficiently removed by Icp55 and thus is the best substrate of Icp55. The efficiency of cleavage is lower for leucine and phenylalanine
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?
additional information
?
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identification of 36 substrates utilizing charge-based fractional diagonal chromatography, enabling the differential quantitation of 1459 nonredundant N-terminal peptides between two Saccharomyces cerevisiae samples within 10 h of LC-MS, starting from only 50 microg of protein per condition and analyzing only 40% of the obtained fractions
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?
additional information
?
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residue Tyr is preferred at P1 position. The enzyme additionally displays Xaa-Pro aminopeptidase activity in vitro
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?
additional information
?
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the enzyme is active towards substrates with proline at P1' position (M-/-PA and Y-/-PA). Icp55 cleaves off bulky residues from N-termini of proteins. Active towards substrates Y-/-AA, Y-/-TA and Y-/-SA
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?
additional information
?
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residue Tyr is preferred at P1 position. The enzyme additionally displays Xaa-Pro aminopeptidase activity in vitro
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?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
Tyr-Ser-Pro-Nfs1 + H2O
Nfs1 + Tyr-Ser-Pro
the enzyme is involved in the processing pathway of yeast Nfs1 during its translocation into the mitochondrial matrix. Nfs1 from Saccharomyces cerevisiae undergoes two steps of proteolytic processing: first the mitochondrial processing peptidase (MPP) cleaves the precursor between Phe33 and Tyr34. Then Icp55 cleaves between Pro36 and Pro37 removing three amino acids residues (Tyr-Ser-Pro)
-
-
?
additional information
?
-
Icp55 is critical for stabilization of the mitochondrial proteome. Icp55 removes an amino acid from a characteristic set of N-termini of preprotein intermediates generated by mitochondrial processing peptidase. Thereby Icp55 converts instable intermediates into stable proteins
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mn2+
additional information
not activating: Mg2+, Ca2+, Co2+, Ni2+, Zn2+
Mn2+
reducing concentration of Mn2+ in reaction buffer from 1 mM to 6 microM reduces the activity of the enzyme by about 60%
Mn2+
the activity of the enzyme depends critically on the presence of Mn2+. Reducing concentration of Mn2+ in reaction buffer from 1 mM to 0.006 mM reduces the activity of the enzyme by about 60%. Other divalent metal ions (Mg2+, Ca2+, Co2+, Ni2+ and Zn2+) fail to fully restore activity of the enzyme
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
transcript ICP55.1 is localized in the mitochondrion
brenda
Icp55 behaves like a protein that is peripherally attached to the mitochondrial inner membrane from the matrix side
brenda
transcript ICP55.2 is localized in the nucleus
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
physiological function
malfunction
icp55DELTA cells are defective in growth on nonfermentable medium at elevated temperature (37°C)
malfunction
Nfs1 purified from the knockout strain, DELTAip55, detected three additional amino acids (Tyr-Ser-Pro), at the N-terminus of Nfs1
physiological function
Icp55 is critical for stabilization of the mitochondrial proteome. The cleavage by Icp55 stabilizes the substrate proteins by removing destabilizing amino acids
physiological function
ICP55 is responsible for the removal of single N-terminal amino acids, and its action explained the -3 arginine processing motif of a number of mitochondrial proteins. ICP55 also removes single amino acids from mitochondrial proteins known to be cleaved at nonconserved arginine sites. Disruption of ICP55 alters mitochondrial protein stability in vitro and changes the protein turnover rate of selected proteins in vivo
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). ICP55_SCHPO
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
486
0
55141
Swiss-Prot
Mitochondrion (Reliability: 2)
ICP55_YEAST
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
511
0
57990
Swiss-Prot
Mitochondrion (Reliability: 2)
A0A7H0KIA4_YARLL
471
0
52445
TrEMBL
Mitochondrion (Reliability: 2)
A0A3G2S334_9BASI
518
0
58188
TrEMBL
Mitochondrion (Reliability: 2)
A0A6J4I586_9ACTN
520
0
51955
TrEMBL
-
W1QK79_OGAPD
Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)
488
0
55212
TrEMBL
Mitochondrion (Reliability: 1)
A0A0F8DCF0_CERFI
415
0
46045
TrEMBL
other Location (Reliability: 2)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
106000
53000
and 106000, gel filtration, truncated variant lacking 42 N-terminal amino acids
106000
and 53000, gel filtration, truncated variant lacking 42 N-terminal amino acids
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
monomer
dimer
2 * 52000, gel filtration, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme with loop dynamics at the dimer interface playing an important role in activity. Dynamics of Icp55 protein between two conformations of dimer are found to be important for activity of the enzyme
dimer
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2 * 52000, gel filtration, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme with loop dynamics at the dimer interface playing an important role in activity. Dynamics of Icp55 protein between two conformations of dimer are found to be important for activity of the enzyme
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monomer
1 * 52000, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme
monomer
and dimer, 1 * 58000 and 2 * 58000, calculated from sequence
monomer
-
1 * 52000, the enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, not monomer, is the active species of the enzyme
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monomer
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and dimer, 1 * 58000 and 2 * 58000, calculated from sequence
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
free enzyme and in complex with inhibitor apstatin. The enzyme exists in a rapid equilibrium between monomer and dimer. The dimer, and not the monomer, is the active species with loop dynamics at the dimer interface playing an important role in activity
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Y284D
Y284D
mutation of a conserved Tyr284 residue located at hinge helix that interacts with its counterpart across the dimer interface. Mutant is a monomer
Y284D
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mutation of a conserved Tyr284 residue located at hinge helix that interacts with its counterpart across the dimer interface. Mutant is a monomer
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli BL21(DE3). Full-length Icp55 construct can not be expressed in the soluble fraction. Two truncated versions, Icp55t1 with 42 amino acid N-terminal truncation and Icp55t2 with 57 amino acid N-terminal truncation, are successfully expressed in soluble forms. All activity assays for Icp55 are reported for Icp55t1 construct
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
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identification of 36 substrates utilizing charge-based fractional diagonal chromatography, enabling the differential quantitation of 1459 nonredundant N-terminal peptides between two Saccharomyces cerevisiae samples within 10 h of LC-MS, starting from only 50 microg of protein per condition and analyzing only 40% of the obtained fractions
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Voegtle, F.N.; Wortelkamp, S.; Zahedi, R.P.; Becker, D.; Leidhold, C.; Gevaert, K.; Kellermann, J.; Voos, W.; Sickmann, A.; Pfanner, N.; Meisinger, C.
Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability
Cell
139
428-439
2009
Saccharomyces cerevisiae (P40051)
brenda
Naamati, A.; Regev-Rudzki, N.; Galperin, S.; Lill, R.; Pines, O.
Dual targeting of Nfs1 and discovery of its novel processing enzyme, Icp55
J. BIOL. CHEM.
284
30200-30208
2009
Saccharomyces cerevisiae (P40051)
brenda
Venne, A.S.; Voegtle, F.N.; Meisinger, C.; Sickmann, A.; Zahedi, R.P.
Novel highly sensitive, specific, and straightforward strategy for comprehensive N-terminal proteomics reveals unknown substrates of the mitochondrial peptidase Icp55
J. Proteome Res.
12
3823-3830
2013
Saccharomyces cerevisiae
brenda
Singh, R.; Goyal, V.D.; Kumar, A.; Sabharwal, N.S.; Makde, R.D.
Crystal structures and biochemical analyses of intermediate cleavage peptidase role of dynamics in enzymatic function
FEBS Lett.
593
443-454
2019
Saccharomyces cerevisiae (P40051), Saccharomyces cerevisiae ATCC 204508 (P40051)
brenda
Carrie, C.; Venne, A.S.; Zahedi, R.P.; Soll, J.
Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana
J. Exp. Bot.
66
2691-2708
2015
Arabidopsis thaliana (F4HZG9)
brenda
Huang, S.; Nelson, C.J.; Li, L.; Taylor, N.L.; Stroeher, E.; Peteriet, J.; Millar, A.H.
Intermediate claevage peptidase55 modifies enzyme amino termini and alters protein stability in Arabidopsis mitochondria
Plant Physiol.
168
415-427
2015
Arabidopsis thaliana (F4HZG9)
brenda
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