4Y7V

Structural analysis of MurU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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Ligand Structure Quality Assessment 


This is version 2.0 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:  
    4Y7T, 4Y7U, 4Y7V

  • 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 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 ...

    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

    From the Interfaculty Institute of Biochemistry (IFIB), thilo.stehle@uni-tuebingen.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleotidyl transferaseA231Pseudomonas putida BIRD-1Mutation(s): 0 
Gene Names: PPUBIRD1_0444
EC: 2.7.7.99
UniProt
Find proteins for Q88QT2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88QT2 
Go to UniProtKB:  Q88QT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88QT2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
491
Query on 491

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

Download Ideal Coordinates CCD File 
E [auth A]IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.35α = 90
b = 72.35β = 90
c = 162.48γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2015-05-06
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary