7NU0 | pdb_00007nu0

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

• PDB DOI: https://doi.org/10.2210/pdb7NU0/pdb

• Classification: LIGASE
• Organism(s): Neisseria gonorrhoeae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-03-11 Released: 2022-09-28 
• Deposition Author(s): Pang, L., Strelkov, S.V., Weeks, S.D.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

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

• PubMed: 36038645 
• DOI: https://doi.org/10.1038/s42003-022-03825-8
• Primary Citation 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.

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Organizational Affiliation: 
• Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium.
Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1041, 3000, Leuven, Belgium.
Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia.
Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1041, 3000, Leuven, Belgium. [e-mail].
Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia. [e-mail].
Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium. [e-mail].
Pledge Therapeutics, Gaston Geenslaan 1, 3001, Leuven, Belgium. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 99.01 kDa 
• Atom Count: 7,169 
• Modeled Residue Count: 865 
• Deposited Residue Count: 877 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine--tRNA ligase	A	877	Neisseria gonorrhoeae	Mutation(s): 1  Gene Names: leuS, NGK_0009 EC: 6.1.1.4
UniProt
Find proteins for B4RNT1 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RNT1  Go to UniProtKB:  B4RNT1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
DCL (Subject of Investigation/LOI)	E [auth A]	2-AMINO-4-METHYL-PENTAN-1-OL C6 H15 N O VPSSPAXIFBTOHY-LURJTMIESA-N
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	B [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	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 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.511	α = 90
b = 81.441	β = 90
c = 215.713	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Pang, L., Strelkov, S.V., Weeks, S.D.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G077814N
Research Foundation - Flanders (FWO)	Belgium	G0A4616A
Research Foundation - Flanders (FWO)	Belgium	1109117N

Revision History  

• 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