6Z64 | pdb_00006z64

Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative

• PDB DOI: https://doi.org/10.2210/pdb6Z64/pdb

• Classification: TRANSFERASE
• Organism(s): Listeria monocytogenes EGD-e
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-05-27 Released: 2021-05-26 
• Deposition Author(s): Gelin, M., Labesse, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

New Chemical Probe Targeting Bacterial NAD Kinase.

Clement, D.A., Leseigneur, C., Gelin, M., Coelho, D., Huteau, V., Lionne, C., Labesse, G., Dussurget, O., Pochet, S.

(2020) Molecules 25

• PubMed: 33105870 
• DOI: https://doi.org/10.3390/molecules25214893
• Primary Citation Related Structures: 
  6Z61, 6Z64, 6Z65


• PubMed Abstract: 
  

  Nicotinamide adenine dinucleotide (NAD) kinases are essential and ubiquitous enzymes involved in the tight regulation of NAD/nicotinamide adenine dinucleotide phosphate (NADP) levels in many metabolic pathways. Consequently, they represent promising therapeutic targets in cancer and antibacterial treatments. We previously reported diadenosine derivatives as NAD kinase inhibitors with bactericidal activities on Staphylococcus aureus . Among them, one compound (namely NKI1 ) was found effective in vivo in a mouse infection model. With the aim to gain detailed knowledge about the selectivity and mechanism of action of this lead compound, we planned to develop a chemical probe that could be used in affinity-based chemoproteomic approaches. Here, we describe the first functionalized chemical probe targeting a bacterial NAD kinase. Aminoalkyl functional groups were introduced on NKI1 for further covalent coupling to an activated Sepharose ^TM matrix. Inhibitory properties of functionalized NKI1 derivatives together with X-ray characterization of their complexes with the NAD kinase led to identify candidate compounds that are amenable to covalent coupling to a matrix.

---

Organizational Affiliation: 
• Institut Pasteur, Unité de Chimie et Biocatalyse, UMR3523 CNRS, 75015 Paris, France.
Faculté des Sciences, Université de Paris, Sorbonne Paris Cité, 75013 Paris, France.
Institut Pasteur, Unité de Recherche Yersinia, 75015 Paris, France.
Centre de Biochimie Structurale (CBS), CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 31.86 kDa 
• Atom Count: 2,246 
• Modeled Residue Count: 262 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD kinase 1	A	272	Listeria monocytogenes EGD-e	Mutation(s): 0  Gene Names: nadK1, lmo0968 EC: 2.7.1.23
UniProt
Find proteins for Q8Y8D7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y8D7  Go to UniProtKB:  Q8Y8D7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q9K (Subject of Investigation/LOI)	C [auth A]	(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl-(3-azanylpropyl)amino]methyl]oxolane-3,4-diol C26 H34 N12 O7 WXECJKFATFMCJP-DQSURDJZSA-N
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.846	α = 90
b = 74.17	β = 90
c = 118.392	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Gelin, M., Labesse, G.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description