2JFF

Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor

• PDB DOI:  https://doi.org/10.2210/pdb2JFF/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2007-02-01 Released: 2007-05-15 
• Deposition Author(s): Kotnik, M., Humljan, J., Contreras-Martel, C., Oblak, M., Kristan, K., Herve, M., Blanot, D., Urleb, U., Gobec, S., Dessen, A., Solmajer, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Structural and Functional Characterization of Enantiomeric Glutamic Acid Derivatives as Potential Transition State Analogue Inhibitors of Murd Ligase.

Kotnik, M., Humljan, J., Contreras-Martel, C., Oblak, M., Kristan, K., Herve, M., Blanot, D., Urleb, U., Gobec, S., Dessen, A., Solmajer, T.

(2007) J Mol Biol 370: 107

• PubMed: 17507028 
• DOI: https://doi.org/10.1016/j.jmb.2007.04.048
• Primary Citation of Related Structures:  
  2JFF, 2JFG, 2JFH


• PubMed Abstract: 
  

Mur ligases play an essential role in the intracellular biosynthesis of bacterial peptidoglycan, the main component of the bacterial cell wall, and represent attractive targets for the design of novel antibacterials. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) catalyses the addition of D-glutamic acid to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA) and is the second in the series of Mur ligases. MurD ligase is highly stereospecific for its substrate, D-glutamic acid (D-Glu). Here, we report the high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, which contain either the D-Glu or the L-Glu moiety. The binding modes of N-sulfonyl-D-Glu and N-sulfonyl-L-Glu derivatives were also characterised kinetically. The results of this study represent an excellent starting point for further development of novel inhibitors of this enzyme.

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Organizational Affiliation: 

Lek Pharmaceuticals d. d., Drug Discovery, Verovskova 57, 1526 Ljubljana, Slovenia. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 48.58 kDa 
• Atom Count: 3,788 
• Modelled Residue Count: 433 
• Deposited Residue Count: 445 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE	A	445	Escherichia coli	Mutation(s): 0  EC: 6.3.2.9
UniProt
Find proteins for P14900 (Escherichia coli (strain K12)) Explore P14900  Go to UniProtKB:  P14900

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LK2	B [auth A]	N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-D-GLUTAMIC ACID C19 H23 N O7 S UAGYXJBYAFGRFR-QGZVFWFLSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
LK2	Binding MOAD:  2JFF	Ki: 2.40e+5 (nM) from 1 assay(s)
	BindingDB:  2JFF	Kd: min: 1.20e+5, max: 2.10e+5 (nM) from 2 assay(s)
		IC50: 2.80e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.215 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.288	α = 90
b = 65.288	β = 90
c = 135.06	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Kotnik, M., Humljan, J., Contreras-Martel, C., Oblak, M., Kristan, K., Herve, M., Blanot, D., Urleb, U., Gobec, S., Dessen, A., Solmajer, T.

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Source and taxonomy