1HR9

Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.

Taylor, A.B.Smith, B.S.Kitada, S.Kojima, K.Miyaura, H.Otwinowski, Z.Ito, A.Deisenhofer, J.

(2001) Structure 9: 615-625

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNIT
A, C, E, G
475Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MAS2 (MIF2)
EC: 3.4.24.64
Find proteins for P11914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P11914
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNIT
B, D, F, H
443Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: MAS1 (MIF1)
EC: 3.4.24.64
Find proteins for P10507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MAS1
Go to UniProtKB:  P10507
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MALATE DEHYDROGENASE
O, P, Q, R
8Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MDH1
EC: 1.1.1.37
Find proteins for P17505 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MDH1
Go to UniProtKB:  P17505
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
E, G
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D, F, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 134.370α = 90.00
b = 178.520β = 90.00
c = 201.950γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance