1XE4 | pdb_00001xe4

Crystal Structure of Weissella viridescens FemX (K36M) Mutant

• PDB DOI: https://doi.org/10.2210/pdb1XE4/pdb

• Classification: TRANSFERASE
• Organism(s): Weissella viridescens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-09-09 Released: 2005-05-31 
• Deposition Author(s): Biarrotte-Sorin, S., Maillard, A.P., Arthur, M., Mayer, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Site-Directed Mutagenesis of the UDP-MurNAc-Pentapeptide-Binding Cavity of the FemX Alanyl Transferase from Weissella viridescens

Maillard, A.P., Biarrotte-Sorin, S., Villet, R., Mesnage, S., Bouhss, A., Sougakoff, W., Mayer, C., Arthur, M.

(2005) J Bacteriol 187: 3833-3838

• PubMed: 15901708 
• DOI: https://doi.org/10.1128/JB.187.11.3833-3838.2005
• Primary Citation Related Structures: 
  1XE4, 1XF8, 1XIX


• PubMed Abstract: 
  

  Weissella viridescens FemX (FemX(Wv)) belongs to the Fem family of nonribosomal peptidyl transferases that use aminoacyl-tRNA as the amino acid donor to synthesize the peptide cross-bridge found in the peptidoglycan of many species of pathogenic gram-positive bacteria. We have recently solved the crystal structure of FemX(Wv) in complex with the peptidoglycan precursor UDP-MurNAc-pentapeptide and report here the site-directed mutagenesis of nine residues located in the binding cavity for this substrate. Two substitutions, Lys36Met and Arg211Met, depressed FemX(Wv) transferase activity below detectable levels without affecting protein folding. Analogues of UDP-MurNAc-pentapeptide lacking the phosphate groups or the C-terminal D-alanyl residues were not substrates of the enzyme. These results indicate that Lys36 and Arg211 participate in a complex hydrogen bond network that connects the C-terminal D-Ala residues to the phosphate groups of UDP-MurNAc-pentapeptide and constrains the substrate in a conformation that is essential for transferase activity.

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Organizational Affiliation: 
• Laboratoire de Recherche Moléculaire sur les Antibiotiques, INSERM U655, Université Paris 6, Paris, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.22 kDa 
• Atom Count: 3,054 
• Modeled Residue Count: 335 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FemX	A	335	Weissella viridescens	Mutation(s): 1  Gene Names: femx EC: 2.3.2.10
UniProt
Find proteins for Q9EY50 (Weissella viridescens) Explore Q9EY50  Go to UniProtKB:  Q9EY50

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.326	α = 90
b = 101.305	β = 103.02
c = 46.331	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-31 
Deposition Author(s): Biarrotte-Sorin, S., Maillard, A.P., Arthur, M., Mayer, C.

Revision History  

• Version 1.0: 2005-05-31
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description