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PDBsum entry 1hr8

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1hr8
Jmol
Contents
Protein chains
452 a.a. *
439 a.a. *
13 a.a. *
Ligands
PHE-PHE-LYS-PRO-
ALA-THR-ARG-THR-
LEU
PHE-PHE-LYS-PRO-
ALA-THR-ARG-THR-
LEU-CYS
LYS-PRO-ALA-THR-
ARG-THR-LEU
EPE ×2
Metals
_ZN ×4
Waters ×4
* Residue conservation analysis
PDB id:
1hr8
Name: Hydrolase
Title: Yeast mitochondrial processing peptidase beta-e73q mutant co with cytochromE C oxidase iv signal peptide
Structure: Mitochondrial processing peptidase alpha subunit. Chain: a, c, e, g. Synonym: alpha-mpp. Engineered: yes. Mitochondrial processing peptidase beta subunit. Chain: b, d, f, h. Synonym: beta-mpp. Engineered: yes. Mutation: yes.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the 24 residue peptide of cytochromE C oxida polypeptide iv was synthesized using standard solid-phase f synthesis methodology
Biol. unit: Trimer (from PQS)
Resolution:
2.70Å     R-factor:   0.229     R-free:   0.264
Authors: A.B.Taylor,B.S.Smith,S.Kitada,K.Kojima,H.Miyaura,Z.Otwinowsk J.Deisenhofer
Key ref:
A.B.Taylor et al. (2001). Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences. Structure, 9, 615-625. PubMed id: 11470436 DOI: 10.1016/S0969-2126(01)00621-9
Date:
21-Dec-00     Release date:   11-Jul-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P11914  (MPPA_YEAST) -  Mitochondrial-processing peptidase subunit alpha
Seq:
Struc:
482 a.a.
452 a.a.*
Protein chains
Pfam   ArchSchema ?
P10507  (MPPB_YEAST) -  Mitochondrial-processing peptidase subunit beta
Seq:
Struc:
462 a.a.
439 a.a.*
Protein chain
Pfam   ArchSchema ?
P04037  (COX4_YEAST) -  Cytochrome c oxidase subunit 4, mitochondrial
Seq:
Struc:
155 a.a.
13 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: Chains A, B, C, D, E, F, G, H: E.C.3.4.24.64  - Mitochondrial processing peptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.
      Cofactor: Zn(2+)
   Enzyme class 3: Chain O: E.C.1.9.3.1  - Cytochrome-c oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4 ferrocytochrome c + O2 + 4 H+ = 4 ferricytochrome c + 2 H2O
4 × ferrocytochrome c
+ O(2)
+ 4 × H(+)
= 4 × ferricytochrome c
+ 2 × H(2)O
      Cofactor: Cu cation
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     mitochondrion   3 terms 
  Biological process     proteolysis   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00621-9 Structure 9:615-625 (2001)
PubMed id: 11470436  
 
 
Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.
A.B.Taylor, B.S.Smith, S.Kitada, K.Kojima, H.Miyaura, Z.Otwinowski, A.Ito, J.Deisenhofer.
 
  ABSTRACT  
 
BACKGROUND: Mitochondrial processing peptidase (MPP) is a metalloendopeptidase that cleaves the N-terminal signal sequences of nuclear-encoded proteins targeted for transport from the cytosol to the mitochondria. Mitochondrial signal sequences vary in length and sequence, but each is cleaved at a single specific site by MPP. The cleavage sites typically contain an arginine at position -2 (in the N-terminal portion) from the scissile peptide bond in addition to other distal basic residues, and an aromatic residue at position +1. Mitochondrial import machinery recognizes amphiphilic helical conformations in signal sequences. However, it is unclear how MPP specifically recognizes diverse presequence substrates. RESULTS: The crystal structures of recombinant yeast MPP and a cleavage-deficient mutant of MPP complexed with synthetic signal peptides have been determined. MPP is a heterodimer; its alpha and beta subunits are homologous to the core II and core I proteins, respectively, of the ubiquinol-cytochrome c oxidoreductase complex. Crystal structures of two different synthetic substrate peptides cocrystallized with the mutant MPP each show the peptide bound in an extended conformation at the active site. Recognition sites for the arginine at position -2 and the +1 aromatic residue are observed. CONCLUSIONS: MPP bound two mitochondrial import presequence peptides in extended conformations in a large polar cavity. The presequence conformations differ from the amphiphilic helical conformation recognized by mitochondrial import components. Our findings suggest that the presequences adopt context-dependent conformations through mitochondrial import and processing, helical for recognition by mitochondrial import machinery and extended for cleavage by the main processing component.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. The Central Cavity of MPP(a) Electrostatic surface representation of MPP contoured at 15 kcal calculated by GRASP [58]. Positive charge is shown as blue and negative charge as red. The flexible loop (residues a284-a301) is circled.(b) A cutaway view of the surface representation of MPP revealing the electrostatic potential of the central cavity

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 615-625) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21151029 M.Y.Lu, and F.Liao (2011).
Interferon-stimulated gene ISG12b2 is localized to the inner mitochondrial membrane and mediates virus-induced cell death.
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20528687 A.M.Shiflett, and P.J.Johnson (2010).
Mitochondrion-related organelles in eukaryotic protists.
  Annu Rev Microbiol, 64, 409-429.  
20130685 J.Thomas, J.Fishovitz, and I.Lee (2010).
Utilization of positional isotope exchange experiments to evaluate reversibility of ATP hydrolysis catalyzed by Escherichia coli Lon protease.
  Biochem Cell Biol, 88, 119-128.  
20729931 O.Schmidt, N.Pfanner, and C.Meisinger (2010).
Mitochondrial protein import: from proteomics to functional mechanisms.
  Nat Rev Mol Cell Biol, 11, 655-667.  
19896952 Q.Guo, M.Manolopoulou, Y.Bian, A.B.Schilling, and W.J.Tang (2010).
Molecular basis for the recognition and cleavages of IGF-II, TGF-alpha, and amylin by human insulin-degrading enzyme.
  J Mol Biol, 395, 430-443.
PDB codes: 2wk3 3e4z 3e50 3hgz
20677216 Y.Yang, B.P.Hubbard, D.A.Sinclair, and Q.Tong (2010).
Characterization of murine SIRT3 transcript variants and corresponding protein products.
  J Cell Biochem, 111, 1051-1058.  
19703392 A.Chacinska, C.M.Koehler, D.Milenkovic, T.Lithgow, and N.Pfanner (2009).
Importing mitochondrial proteins: machineries and mechanisms.
  Cell, 138, 628-644.  
19913481 A.E.Aleshin, S.Gramatikova, G.L.Hura, A.Bobkov, A.Y.Strongin, B.Stec, J.A.Tainer, R.C.Liddington, and J.W.Smith (2009).
Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.
  Structure, 17, 1465-1475.
PDB code: 3hdi
19421406 A.Parcellier, L.A.Tintignac, E.Zhuravleva, B.Dummler, D.P.Brazil, D.Hynx, P.Cron, S.Schenk, V.Olivieri, and B.A.Hemmings (2009).
The Carboxy-Terminal Modulator Protein (CTMP) regulates mitochondrial dynamics.
  PLoS ONE, 4, e5471.  
19837041 F.N.Vögtle, S.Wortelkamp, R.P.Zahedi, D.Becker, C.Leidhold, K.Gevaert, J.Kellermann, W.Voos, A.Sickmann, N.Pfanner, and C.Meisinger (2009).
Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability.
  Cell, 139, 428-439.  
18470479 E.Malito, R.E.Hulse, and W.J.Tang (2008).
Amyloid beta-degrading cryptidases: insulin degrading enzyme, presequence peptidase, and neprilysin.
  Cell Mol Life Sci, 65, 2574-2585.  
18768474 M.J.Page, and E.Di Cera (2008).
Evolution of peptidase diversity.
  J Biol Chem, 283, 30010-30014.  
18784075 O.Gakh, D.Y.Smith, and G.Isaya (2008).
Assembly of the Iron-binding Protein Frataxin in Saccharomyces cerevisiae Responds to Dynamic Changes in Mitochondrial Iron Influx and Stress Level.
  J Biol Chem, 283, 31500-31510.  
19096520 O.Smíd, A.Matusková, S.R.Harris, T.Kucera, M.Novotný, L.Horváthová, I.Hrdý, E.Kutejová, R.P.Hirt, T.M.Embley, J.Janata, and J.Tachezy (2008).
Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis.
  PLoS Pathog, 4, e1000243.  
18095874 Y.Huet, J.Strassner, and A.Schaller (2008).
Cloning, expression and characterization of insulin-degrading enzyme from tomato (Solanum lycopersicum).
  Biol Chem, 389, 91-98.  
17959599 A.Mukhopadhyay, C.S.Yang, B.Wei, and H.Weiner (2007).
Precursor Protein Is Readily Degraded in Mitochondrial Matrix Space if the Leader Is Not Processed by Mitochondrial Processing Peptidase.
  J Biol Chem, 282, 37266-37275.  
17581127 C.V.Galmozzi, M.J.Fernández-Avila, J.C.Reyes, F.J.Florencio, and M.I.Muro-Pastor (2007).
The ammonium-inactivated cyanobacterial glutamine synthetase I is reactivated in vivo by a mechanism involving proteolytic removal of its inactivating factors.
  Mol Microbiol, 65, 166-179.  
17696772 D.Milenkovic, J.Müller, D.Stojanovski, N.Pfanner, and A.Chacinska (2007).
Diverse mechanisms and machineries for import of mitochondrial proteins.
  Biol Chem, 388, 891-897.  
17613531 H.Im, M.Manolopoulou, E.Malito, Y.Shen, J.Zhao, M.Neant-Fery, C.Y.Sun, S.C.Meredith, S.S.Sisodia, M.A.Leissring, and W.J.Tang (2007).
Structure of substrate-free human insulin-degrading enzyme (IDE) and biophysical analysis of ATP-induced conformational switch of IDE.
  J Biol Chem, 282, 25453-25463.
PDB codes: 2jbu 2jg4
17825565 M.J.Baker, A.E.Frazier, J.M.Gulbis, and M.T.Ryan (2007).
Mitochondrial protein-import machinery: correlating structure with function.
  Trends Cell Biol, 17, 456-464.  
17074076 M.Ponpuak, M.Klemba, M.Park, I.Y.Gluzman, G.K.Lamppa, and D.E.Goldberg (2007).
A role for falcilysin in transit peptide degradation in the Plasmodium falciparum apicoplast.
  Mol Microbiol, 63, 314-334.  
17542912 M.T.Brown, H.M.Goldstone, F.Bastida-Corcuera, M.G.Delgadillo-Correa, A.G.McArthur, and P.J.Johnson (2007).
A functionally divergent hydrogenosomal peptidase with protomitochondrial ancestry.
  Mol Microbiol, 64, 1154-1163.  
17446895 O.Emanuelsson, S.Brunak, G.von Heijne, and H.Nielsen (2007).
Locating proteins in the cell using TargetP, SignalP and related tools.
  Nat Protoc, 2, 953-971.  
17158683 S.Kitada, T.Uchiyama, T.Funatsu, Y.Kitada, T.Ogishima, and A.Ito (2007).
A protein from a parasitic microorganism, Rickettsia prowazekii, can cleave the signal sequences of proteins targeting mitochondria.
  J Bacteriol, 189, 844-850.  
16780565 C.Argueta, K.Yuksek, R.Patel, and M.L.Summers (2006).
Identification of Nostoc punctiforme akinete-expressed genes using differential display.
  Mol Microbiol, 61, 748-757.  
16601675 K.A.Johnson, S.Bhushan, A.Ståhl, B.M.Hallberg, A.Frohn, E.Glaser, and T.Eneqvist (2006).
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  EMBO J, 25, 1977-1986.
PDB code: 2fge
  16504157 K.M.Honeychurch, C.M.Byrd, and D.E.Hruby (2006).
Mutational analysis of the potential catalytic residues of the VV G1L metalloproteinase.
  Virol J, 3, 7.  
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Regulation of mitochondrial morphology through proteolytic cleavage of OPA1.
  EMBO J, 25, 2966-2977.  
17099692 R.Albrecht, P.Rehling, A.Chacinska, J.Brix, S.A.Cadamuro, R.Volkmer, B.Guiard, N.Pfanner, and K.Zeth (2006).
The Tim21 binding domain connects the preprotein translocases of both mitochondrial membranes.
  EMBO Rep, 7, 1233-1238.
PDB code: 2ciu
17051221 Y.Shen, A.Joachimiak, M.R.Rosner, and W.J.Tang (2006).
Structures of human insulin-degrading enzyme reveal a new substrate recognition mechanism.
  Nature, 443, 870-874.
PDB codes: 2g47 2g48 2g49 2g54 2g56
15634341 C.G.Wilson, T.Kajander, and L.Regan (2005).
The crystal structure of NlpI. A prokaryotic tetratricopeptide repeat protein with a globular fold.
  FEBS J, 272, 166-179.
PDB code: 1xnf
15870080 G.Ondrovicová, T.Liu, K.Singh, B.Tian, H.Li, O.Gakh, D.Perecko, J.Janata, Z.Granot, J.Orly, E.Kutejová, and C.K.Suzuki (2005).
Cleavage site selection within a folded substrate by the ATP-dependent lon protease.
  J Biol Chem, 280, 25103-25110.  
15775970 H.Otera, S.Ohsakaya, Z.Nagaura, N.Ishihara, and K.Mihara (2005).
Export of mitochondrial AIF in response to proapoptotic stimuli depends on processing at the intermembrane space.
  EMBO J, 24, 1375-1386.  
16305741 S.Wongtangtintharn, H.Oku, H.Iwasaki, M.Inafuku, T.Toda, and T.Yanagita (2005).
Incorporation of branched-chain fatty acid into cellular lipids and caspase-independent apoptosis in human breast cancer cell line, SKBR-3.
  Lipids Health Dis, 4, 29.  
14973134 N.Wiedemann, A.E.Frazier, and N.Pfanner (2004).
The protein import machinery of mitochondria.
  J Biol Chem, 279, 14473-14476.  
15232570 P.Rehling, K.Brandner, and N.Pfanner (2004).
Mitochondrial import and the twin-pore translocase.
  Nat Rev Mol Cell Biol, 5, 519-530.  
12551941 A.Mukhopadhyay, T.S.Heard, X.Wen, P.K.Hammen, and H.Weiner (2003).
Location of the actual signal in the negatively charged leader sequence involved in the import into the mitochondrial matrix space.
  J Biol Chem, 278, 13712-13718.  
12876284 C.E.Murata, and D.E.Goldberg (2003).
Plasmodium falciparum falcilysin: a metalloprotease with dual specificity.
  J Biol Chem, 278, 38022-38028.  
12433926 S.Kitada, E.Yamasaki, K.Kojima, and A.Ito (2003).
Determination of the cleavage site of the presequence by mitochondrial processing peptidase on the substrate binding scaffold and the multiple subsites inside a molecular cavity.
  J Biol Chem, 278, 1879-1885.  
12888578 S.Richter, and G.K.Lamppa (2003).
Structural properties of the chloroplast stromal processing peptidase required for its function in transit peptide removal.
  J Biol Chem, 278, 39497-39502.  
12185844 A.Chacinska, N.Pfanner, and C.Meisinger (2002).
How mitochondria import hydrophilic and hydrophobic proteins.
  Trends Cell Biol, 12, 299-303.  
11967360 A.Mukhopadhyay, P.Hammen, M.Waltner-Law, and H.Weiner (2002).
Timing and structural consideration for the processing of mitochondrial matrix space proteins by the mitochondrial processing peptidase (MPP).
  Protein Sci, 11, 1026-1035.  
12235156 F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, and D.Xia (2002).
Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.
  J Biol Chem, 277, 46753-46762.
PDB codes: 1mbu 1mbv 1mbx
11952898 G.Buchanan, E.de Leeuw, N.R.Stanley, M.Wexler, B.C.Berks, F.Sargent, and T.Palmer (2002).
Functional complexity of the twin-arginine translocase TatC component revealed by site-directed mutagenesis.
  Mol Microbiol, 43, 1457-1470.  
12383789 N.Pfanner, and N.Wiedemann (2002).
Mitochondrial protein import: two membranes, three translocases.
  Curr Opin Cell Biol, 14, 400-411.  
12235143 S.Richter, and G.K.Lamppa (2002).
Determinants for removal and degradation of transit peptides of chloroplast precursor proteins.
  J Biol Chem, 277, 43888-43894.  
12138093 S.Vial, H.Lu, S.Allen, P.Savory, D.Thornton, J.Sheehan, and K.Tokatlidis (2002).
Assembly of Tim9 and Tim10 into a functional chaperone.
  J Biol Chem, 277, 36100-36108.  
12410806 T.Kamphausen, J.Fanghänel, D.Neumann, B.Schulz, and J.U.Rahfeld (2002).
Characterization of Arabidopsis thaliana AtFKBP42 that is membrane-bound and interacts with Hsp90.
  Plant J, 32, 263-276.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.