4Y7U

Structural analysis of MurU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the N-Acetylmuramic Acid alpha-1-Phosphate (MurNAc-alpha 1-P) Uridylyltransferase MurU, a Minimal Sugar Nucleotidyltransferase and Potential Drug Target Enzyme in Gram-negative Pathogens.

Renner-Schneck, M.Hinderberger, I.Gisin, J.Exner, T.Mayer, C.Stehle, T.

(2015) J.Biol.Chem. 290: 10804-10813

  • DOI: 10.1074/jbc.M114.620989
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The N-acetylmuramic acid α-1-phosphate (MurNAc-α1-P) uridylyltransferase MurU catalyzes the synthesis of uridine diphosphate (UDP)-MurNAc, a crucial precursor of the bacterial peptidoglycan cell wall. MurU is part of a recently identified cell wall r ...

    The N-acetylmuramic acid α-1-phosphate (MurNAc-α1-P) uridylyltransferase MurU catalyzes the synthesis of uridine diphosphate (UDP)-MurNAc, a crucial precursor of the bacterial peptidoglycan cell wall. MurU is part of a recently identified cell wall recycling pathway in Gram-negative bacteria that bypasses the general de novo biosynthesis of UDP-MurNAc and contributes to high intrinsic resistance to the antibiotic fosfomycin, which targets UDP-MurNAc de novo biosynthesis. To provide insights into substrate binding and specificity, we solved crystal structures of MurU of Pseudomonas putida in native and ligand-bound states at high resolution. With the help of these structures, critical enzyme-substrate interactions were identified that enable tight binding of MurNAc-α1-P to the active site of MurU. The MurU structures define a "minimal domain" required for general nucleotidyltransferase activity. They furthermore provide a structural basis for the chemical design of inhibitors of MurU that could serve as novel drugs in combination therapy against multidrug-resistant Gram-negative pathogens.


    Organizational Affiliation

    Institute of Pharmacy, University of Tübingen, 72076 Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Biology, and.,From the Interfaculty Institute of Biochemistry (IFIB), thilo.stehle@uni-tuebingen.de.,From the Interfaculty Institute of Biochemistry (IFIB).,Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Department of Biology, and christoph.mayer@uni-tuebingen.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleotidyl transferase
A
231Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)Mutation(s): 0 
Gene Names: murU
EC: 2.7.7.99
Find proteins for Q88QT2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440))
Go to UniProtKB:  Q88QT2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2KH
Query on 2KH

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Download CCD File 
A
5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
C9 H16 N3 O14 P3
OZIBFYOFLVBDIY-XVFCMESISA-N
 Ligand Interaction
491
Query on 491

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Download CCD File 
A
2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
C11 H20 N O11 P
DTSXRQWOCZUNPL-YVNCZSHWSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.228 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.750α = 90.00
b = 72.750β = 90.00
c = 163.130γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Type: Database references
  • Version 1.2: 2015-05-06
    Type: Database references