7NU0

Crystal Structure of Neisseria gonorrhoeae LeuRS L550A mutant in Complex with ATP and L-leucinol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip.

Pang, L.Zanki, V.Strelkov, S.V.Van Aerschot, A.Gruic-Sovulj, I.Weeks, S.D.

(2022) Commun Biol 5: 883-883

  • DOI: https://doi.org/10.1038/s42003-022-03825-8
  • Primary Citation of Related Structures:  
    7NTY, 7NTZ, 7NU0, 7NU1, 7NU2, 7NU3, 7NU4, 7NU5, 7NU6, 7NU7, 7NU8, 7NU9, 7NUA, 7NUB, 7NUC

  • PubMed Abstract: 

    To correctly aminoacylate tRNA Leu , leucyl-tRNA synthetase (LeuRS) catalyzes three reactions: activation of leucine by ATP to form leucyl-adenylate (Leu-AMP), transfer of this amino acid to tRNA Leu and post-transfer editing of any mischarged product. Although LeuRS has been well characterized biochemically, detailed structural information is currently only available for the latter two stages of catalysis. We have solved crystal structures for all enzymatic states of Neisseria gonorrhoeae LeuRS during Leu-AMP formation. These show a cycle of dramatic conformational changes, involving multiple domains, and correlate with an energetically unfavorable peptide-plane flip observed in the active site of the pre-transition state structure. Biochemical analyses, combined with mutant structural studies, reveal that this backbone distortion acts as a trigger, temporally compartmentalizing the first two catalytic steps. These results unveil the remarkable effect of this small structural alteration on the global dynamics and activity of the enzyme.


  • Organizational Affiliation

    Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine--tRNA ligase877Neisseria gonorrhoeaeMutation(s): 1 
Gene Names: leuSNGK_0009
EC: 6.1.1.4
UniProt
Find proteins for B4RNT1 (Neisseria gonorrhoeae (strain NCCP11945))
Explore B4RNT1 
Go to UniProtKB:  B4RNT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4RNT1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
DCL (Subject of Investigation/LOI)
Query on DCL

Download Ideal Coordinates CCD File 
E [auth A]2-AMINO-4-METHYL-PENTAN-1-OL
C6 H15 N O
VPSSPAXIFBTOHY-LURJTMIESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.511α = 90
b = 81.441β = 90
c = 215.713γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG077814N
Research Foundation - Flanders (FWO)BelgiumG0A4616A
Research Foundation - Flanders (FWO)Belgium1109117N

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 2.1: 2024-01-31
    Changes: Refinement description