5LUZ

Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Mechanism of Peptide Binding and Cleavage by the Human Mitochondrial Peptidase Neurolysin.

Teixeira, P.F.Masuyer, G.Pinho, C.M.Branca, R.M.M.Kmiec, B.Wallin, C.Warmlander, S.K.T.S.Berntsson, R.P.Ankarcrona, M.Graslund, A.Lehtio, J.Stenmark, P.Glaser, E.

(2018) J Mol Biol 430: 348-362

  • DOI: https://doi.org/10.1016/j.jmb.2017.11.011
  • Primary Citation of Related Structures:  
    5LUZ

  • PubMed Abstract: 

    Proteolysis plays an important role in mitochondrial biogenesis, from the processing of newly imported precursor proteins to the degradation of mitochondrial targeting peptides. Disruption of peptide degradation activity in yeast, plant and mammalian mitochondria is known to have deleterious consequences for organism physiology, highlighting the important role of mitochondrial peptidases. In the present work, we show that the human mitochondrial peptidase neurolysin (hNLN) can degrade mitochondrial presequence peptides as well as other fragments up to 19 amino acids long. The crystal structure of hNLN E475Q in complex with the products of neurotensin cleavage at 2.7Å revealed a closed conformation with an internal cavity that restricts substrate length and highlighted the mechanism of enzyme opening/closing that is necessary for substrate binding and catalytic activity. Analysis of peptide degradation in vitro showed that hNLN cooperates with presequence protease (PreP or PITRM1) in the degradation of long targeting peptides and amyloid-β peptide, Aβ1-40, associated with Alzheimer disease, particularly cleaving the hydrophobic fragment Aβ35-40. These findings suggest that a network of proteases may be required for complete degradation of peptides localized in mitochondria.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden. Electronic address: pedro@dbb.su.se.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neurolysin, mitochondrial
A, B
686Homo sapiensMutation(s): 1 
Gene Names: NLNAGTBPKIAA1226
EC: 3.4.24.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYT8 (Homo sapiens)
Explore Q9BYT8 
Go to UniProtKB:  Q9BYT8
PHAROS:  Q9BYT8
GTEx:  ENSG00000123213 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYT8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PRO-ARG-ARG-PRO neurotensin fragmentC,
D,
E [auth P],
F [auth Q]
13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P30990 (Homo sapiens)
Explore P30990 
Go to UniProtKB:  P30990
PHAROS:  P30990
GTEx:  ENSG00000133636 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30990
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.329α = 90
b = 131.329β = 90
c = 195.229γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2014-5667

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2018-02-07
    Changes: Structure summary
  • Version 1.3: 2018-02-14
    Changes: Database references
  • Version 2.0: 2020-03-11
    Changes: Polymer sequence
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-10-23
    Changes: Structure summary