1HR6

Yeast Mitochondrial Processing Peptidase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

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

  • DOI: 10.1016/s0969-2126(01)00621-9
  • Primary Citation of Related Structures:  
    1HR6, 1HR7, 1HR8, 1HR9

  • 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 sequence, but each is cleaved at a single specific site by MPP ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL PROCESSING PEPTIDASE ALPHA SUBUNITA, C, E, G475Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.24.64
UniProt
Find proteins for P11914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11914 
Go to UniProtKB:  P11914
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11914
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MITOCHONDRIAL PROCESSING PEPTIDASE BETA SUBUNITB, D, F, H443Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.24.64
UniProt
Find proteins for P10507 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P10507 
Go to UniProtKB:  P10507
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10507
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
Download Ideal Coordinates CCD File 
I [auth A],
M [auth G]		4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J [auth B],
K [auth D],
L [auth F],
N [auth H]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.18α = 90
b = 178.5β = 90
c = 202.07γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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