Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 48580.98 
• Atom Count: 3309 
• Residue Count: 445 
• Unique protein chains: 1

2JFF

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

• DOI: 10.2210/pdb2JFF/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli DH5[alpha]


• 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 

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: 10.1016/j.jmb.2007.04.048
• Primary Citation of Related Structures:  
  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]

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
LK2	A	N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-D-GLUTAMIC ACID C19 H23 N O7 S UAGYXJBYAFGRFR-QGZVFWFLSA-N
SO4	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LK2	Kd: 120000 - 210000 nM (100) BINDINGDB
LK2	IC50: 280000 nM (100) BINDINGDB
LK2	Ki: 240000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 65.288	α = 90.00
b = 65.288	β = 90.00
c = 135.060	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-01 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-31
  Type: Source and taxonomy