4NGE

Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.704 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis of substrate recognition and degradation by human presequence protease.

King, J.V.Liang, W.G.Scherpelz, K.P.Schilling, A.B.Meredith, S.C.Tang, W.J.

(2014) Structure 22: 996-1007

  • DOI: 10.1016/j.str.2014.05.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human presequence protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing an ∼13,300-Å(3) catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochond ...

    Human presequence protease (hPreP) is an M16 metalloprotease localized in mitochondria. There, hPreP facilitates proteostasis by utilizing an ∼13,300-Å(3) catalytic chamber to degrade a diverse array of potentially toxic peptides, including mitochondrial presequences and β-amyloid (Aβ), the latter of which contributes to Alzheimer disease pathogenesis. Here, we report crystal structures for hPreP alone and in complex with Aβ, which show that hPreP uses size exclusion and charge complementation for substrate recognition. These structures also reveal hPreP-specific features that permit a diverse array of peptides, with distinct distributions of charged and hydrophobic residues, to be specifically captured, cleaved, and have their amyloidogenic features destroyed. SAXS analysis demonstrates that hPreP in solution exists in dynamic equilibrium between closed and open states, with the former being preferred. Furthermore, Aβ binding induces the closed state and hPreP dimerization. Together, these data reveal the molecular basis for flexible yet specific substrate recognition and degradation by hPreP.


    Organizational Affiliation

    Ben May Department for Cancer Research, The University of Chicago, 929 E. 57(th) Street, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Presequence protease, mitochondrial
A
1014Homo sapiensMutation(s): 1 
Gene Names: PITRM1 (KIAA1104, MP1)
EC: 3.4.24.-
Find proteins for Q5JRX3 (Homo sapiens)
Go to Gene View: PITRM1
Go to UniProtKB:  Q5JRX3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-amyloid protein 40
B, E
40Homo sapiensMutation(s): 0 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Beta-amyloid protein 40
C, F
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Presequence protease, mitochondrial
D
1014Homo sapiensMutation(s): 1 
Gene Names: PITRM1 (KIAA1104, MP1)
EC: 3.4.24.-
Find proteins for Q5JRX3 (Homo sapiens)
Go to Gene View: PITRM1
Go to UniProtKB:  Q5JRX3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
CAS
Query on CAS
A, D
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
UNK
Query on UNK
C, F
L-PEPTIDE LINKINGC4 H9 N O2

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MLY
Query on MLY
A, D
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.704 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 247.275α = 90.00
b = 86.183β = 127.56
c = 158.611γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-05-21
    Type: Database references
  • Version 1.2: 2014-07-09
    Type: Database references
  • Version 1.3: 2014-07-23
    Type: Database references