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 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: 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 ...

    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: e_glaser@dbb.su.se.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neurolysin, mitochondrialA, B686Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYT8
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PRO-ARG-ARG-PRO neurotensin fragmentC,
D,
E [auth P],
F [auth Q]
13Homo sapiensMutation(s): 0 
Gene Names: NTS
UniProt & NIH Common Fund Data Resources
Find proteins for P30990 (Homo sapiens)
Explore P30990 
Go to UniProtKB:  P30990
PHAROS:  P30990
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30990
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
C,
D,
E [auth P],
F [auth Q]
L-PEPTIDE LINKINGC5 H7 N O3GLN
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

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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