PDBsum entry 2fge

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protein ligands metals Protein-protein interface(s) links
Hydrolase, plant protein PDB id
Protein chains
979 a.a. *
_MG ×4
_ZN ×2
_CL ×2
Waters ×948
* Residue conservation analysis
PDB id:
Name: Hydrolase, plant protein
Title: Crystal structure of presequence protease prep from arabidopsis thaliana
Structure: Zinc metalloprotease (insulinase family). Chain: a, b. Synonym: presequence protease prep. Atprep2. Metalloendopeptidase. Atprep1/atznmp. Engineered: yes. Mutation: yes. Nonspecific peptide aaltra. Chain: d, e. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes
Biol. unit: Dimer (from PQS)
2.10Å     R-factor:   0.209     R-free:   0.256
Authors: T.Eneqvist,K.A.Johnson
Key ref:
K.A.Johnson et al. (2006). The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis. EMBO J, 25, 1977-1986. PubMed id: 16601675 DOI: 10.1038/sj.emboj.7601080
21-Dec-05     Release date:   16-May-06    
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Protein chains
Pfam   ArchSchema ?
Q9LJL3  (PREP1_ARATH) -  Presequence protease 1, chloroplastic/mitochondrial
1080 a.a.
979 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     apoplast   7 terms 
  Biological process     chloroplast organization   6 terms 
  Biochemical function     catalytic activity     7 terms  


DOI no: 10.1038/sj.emboj.7601080 EMBO J 25:1977-1986 (2006)
PubMed id: 16601675  
The closed structure of presequence protease PreP forms a unique 10,000 Angstroms3 chamber for proteolysis.
K.A.Johnson, S.Bhushan, A.Ståhl, B.M.Hallberg, A.Frohn, E.Glaser, T.Eneqvist.
Presequence protease PreP is a novel protease that degrades targeting peptides as well as other unstructured peptides in both mitochondria and chloroplasts. The first structure of PreP from Arabidopsis thaliana refined at 2.1 Angstroms resolution shows how the 995-residue polypeptide forms a unique proteolytic chamber of more than 10,000 Angstroms(3) in which the active site resides. Although there is no visible opening to the chamber, a peptide is bound to the active site. The closed conformation places previously unidentified residues from the C-terminal domain at the active site, separated by almost 800 residues in sequence to active site residues located in the N-terminal domain. Based on the structure, a novel mechanism for proteolysis is proposed involving hinge-bending motions that cause the protease to open and close in response to substrate binding. In support of this model, cysteine double mutants designed to keep the chamber covalently locked show no activity under oxidizing conditions. The manner in which substrates are processed inside the chamber is reminiscent of the proteasome; therefore, we refer to this protein as a peptidasome.
  Selected figure(s)  
Figure 5.
Figure 5 Proposed mechanism for the PreP peptidasome substrate binding and release.
Figure 6.
Figure 6 AtPreP1 is inactive if locked in a closed conformation. (A) Schematic representation of the AtPreP1 cysteine double mutants K171C-G852C (C1), K179C-Q810C (C2), E345C-S682C (C3) and A331C-N615C (C4) under reducing and oxidizing conditions. Proteolytic activity of native (wt) AtPreP1 and the cysteine double mutants measured as the degradation of N[5.7]pF[1] (2–54) under reducing (B) and oxidizing conditions (C) and degradation of the P1 peptide under reducing (D) and oxidizing conditions (E).
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 1977-1986) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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
19995731 A.K.Berglund, E.Spånning, H.Biverståhl, G.Maddalo, C.Tellgren-Roth, L.Mäler, and E.Glaser (2009).
Dual Targeting to Mitochondria and Chloroplasts: Characterization of Thr-tRNA Synthetase Targeting Peptide.
  Mol Plant, 2, 1298-1309.  
19701724 S.Nilsson Cederholm, H.G.Bäckman, P.Pesaresi, D.Leister, and E.Glaser (2009).
Deletion of an organellar peptidasome PreP affects early development in Arabidopsis thaliana.
  Plant Mol Biol, 71, 497-508.  
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.  
18583346 Q.Guo, J.E.Jureller, J.T.Warren, E.Solomaha, J.Florián, and W.J.Tang (2008).
Protein-protein docking and analysis reveal that two homologous bacterial adenylyl cyclase toxins interact with calmodulin differently.
  J Biol Chem, 283, 23836-23845.  
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
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.  
17241197 S.A.Ralph (2007).
Subcellular multitasking - multiple destinations and roles for the Plasmodium falcilysin protease.
  Mol Microbiol, 63, 309-313.  
16849325 A.Falkevall, N.Alikhani, S.Bhushan, P.F.Pavlov, K.Busch, K.A.Johnson, T.Eneqvist, L.Tjernberg, M.Ankarcrona, and E.Glaser (2006).
Degradation of the amyloid beta-protein by the novel mitochondrial peptidasome, PreP.
  J Biol Chem, 281, 29096-29104.  
17081117 E.Glaser, S.Nilsson, and S.Bhushan (2006).
Two novel mitochondrial and chloroplastic targeting-peptide-degrading peptidasomes in A. thaliana, AtPreP1 and AtPreP2.
  Biol Chem, 387, 1441-1447.  
16895479 S.Bhushan, K.A.Johnson, T.Eneqvist, and E.Glaser (2006).
Proteolytic mechanism of a novel mitochondrial and chloroplastic PreP peptidasome.
  Biol Chem, 387, 1087-1090.  
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.