4L3T

Crystal Structure of Substrate-free Human Presequence Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    4NGE, 4L3T

  • 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 mitochondrial presequences and β-amyloid (Aβ), the latter of which contributes to Alzheimer disease pathogenesis ...

    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. Electronic address: wtang@uchicago.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Presequence protease, mitochondrialA1014Homo sapiensMutation(s): 1 
Gene Names: KIAA1104MP1PITRM1PREP
EC: 3.4.24
Find proteins for Q5JRX3 (Homo sapiens)
Explore Q5JRX3 
Go to UniProtKB:  Q5JRX3
NIH Common Fund Data Resources
PHAROS:  Q5JRX3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Presequence protease, mitochondrialB1014Homo sapiensMutation(s): 1 
Gene Names: KIAA1104MP1PITRM1PREP
EC: 3.4.24
Find proteins for Q5JRX3 (Homo sapiens)
Explore Q5JRX3 
Go to UniProtKB:  Q5JRX3
NIH Common Fund Data Resources
PHAROS:  Q5JRX3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], I [auth A], L [auth B], M [auth B], N [auth B], V [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], K [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , J [auth A] , O [auth B] , P [auth B] , Q [auth B] , R [auth B] , 
F [auth A],  G [auth A],  H [auth A],  J [auth A],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  W [auth B],  X [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
AL-PEPTIDE LINKINGC5 H12 As N O2 SCYS
MLY
Query on MLY
AL-PEPTIDE LINKINGC8 H18 N2 O2LYS
MLZ
Query on MLZ
AL-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 245.782α = 90
b = 85.093β = 127.54
c = 158.459γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references
  • Version 1.2: 2014-05-21
    Changes: Database references
  • Version 1.3: 2014-07-09
    Changes: Database references
  • Version 1.4: 2014-07-23
    Changes: Database references