5D8N

Tomato leucine aminopeptidase mutant - K354E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural insights into chaperone-activity enhancement by a K354E mutation in tomato acidic leucine aminopeptidase.

DuPrez, K.T.Scranton, M.A.Walling, L.L.Fan, L.

(2016) Acta Crystallogr D Struct Biol 72: 694-702

  • DOI: https://doi.org/10.1107/S205979831600509X
  • Primary Citation of Related Structures:  
    5D8N

  • PubMed Abstract: 

    Tomato plants express acidic leucine aminopeptidase (LAP-A) in response to various environmental stressors. LAP-A not only functions as a peptidase for diverse peptide substrates, but also displays chaperone activity. A K354E mutation has been shown to abolish the peptidase activity but to enhance the chaperone activity of LAP-A. To better understand this moonlighting function of LAP-A, the crystal structure of the K354E mutant was determined at 2.15 Å resolution. The structure reveals that the K354E mutation destabilizes an active-site loop and causes significant rearrangement of active-site residues, leading to loss of the catalytic metal-ion coordination required for the peptidase activity. Although the mutant was crystallized in the same hexameric form as wild-type LAP-A, gel-filtration chromatography revealed an apparent shift from the hexamer to lower-order oligomers for the K354E mutant, showing a mixture of monomers to trimers in solution. In addition, surface-probing assays indicated that the K354E mutant has more accessible hydrophobic areas than wild-type LAP-A. Consistently, computational thermodynamic estimations of the interfaces between LAP-A monomers suggest that increased exposure of hydrophobic surfaces occurs upon hexamer breakdown. These results suggest that the K354E mutation disrupts the active-site loop, which also contributes to the hexameric assembly, and destabilizes the hexamers, resulting in much greater hydrophobic areas accessible for efficient chaperone activity than in the wild-type LAP-A.


  • Organizational Affiliation

    Department of Biochemistry, University of California Riverside, Riverside, CA 92521, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine aminopeptidase 1, chloroplastic
A, B, C
529Solanum lycopersicumMutation(s): 1 
Gene Names: LAPA1LAPLAP2
EC: 3.4.11.1 (PDB Primary Data), 3.4.11.5 (PDB Primary Data)
UniProt
Find proteins for Q10712 (Solanum lycopersicum)
Explore Q10712 
Go to UniProtKB:  Q10712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10712
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth B]
K [auth B]
L [auth B]
M [auth B]
T [auth C]
J [auth B],
K [auth B],
L [auth B],
M [auth B],
T [auth C],
U [auth C],
V [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth C],
I [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
N [auth B]
O [auth B]
D [auth A],
E [auth A],
F [auth A],
N [auth B],
O [auth B],
P [auth B],
W [auth C],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
Q [auth B]
R [auth B]
S [auth B]
G [auth A],
H [auth A],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.112α = 90
b = 165.193β = 90
c = 168.275γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesIOS 0725093

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-11-01
    Changes: Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description