6FTB

Staphylococcus aureus monofunctional glycosyltransferase in complex with moenomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization.

Punekar, A.S.Samsudin, F.Lloyd, A.J.Dowson, C.G.Scott, D.J.Khalid, S.Roper, D.I.

(2018) Cell Surf 2: 54-66

  • DOI: 10.1016/j.tcsw.2018.06.002
  • Primary Citation of Related Structures:  
    6FTB

  • PubMed Abstract: 
  • Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the essential polymerization of lipid II into linear glycan chains required for peptidoglycan biosynthesis. The PGT domain is composed of a large head subdomain and a smaller jaw subdomain and can be potently inhibited by the antibiotic moenomycin A (MoeA) ...

    Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the essential polymerization of lipid II into linear glycan chains required for peptidoglycan biosynthesis. The PGT domain is composed of a large head subdomain and a smaller jaw subdomain and can be potently inhibited by the antibiotic moenomycin A (MoeA). We present an X-ray structure of the MoeA-bound Staphylococcus aureus monofunctional PGT enzyme, revealing electron density for a second MoeA bound to the jaw subdomain as well as the PGT donor site. Isothermal titration calorimetry confirms two drug-binding sites with markedly different affinities and positive cooperativity. Hydrophobic cluster analysis suggests that the membrane-interacting surface of the jaw subdomain has structural and physicochemical properties similar to amphipathic cationic α -helical antimicrobial peptides for lipid II recognition and binding. Furthermore, molecular dynamics simulations of the drug-free and -bound forms of the enzyme demonstrate the importance of the jaw subdomain movement for lipid II selection and polymerization process and provide molecular-level insights into the mechanism of peptidoglycan biosynthesis by PGTs.


    Related Citations: 
    • Characterization of the active site of S. aureus monofunctional glycosyltransferase (Mtg) by site-directed mutation and structural analysis of the protein complexed with moenomycin.
      Heaslet, H., Shaw, B., Mistry, A., Miller, A.A.
      (2009) J Struct Biol 167: 129

    Organizational Affiliation

    School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Monofunctional glycosyltransferaseA210Staphylococcus aureus MW2Mutation(s): 0 
Gene Names: mgtMW1814
EC: 2.4.1.129
UniProt
Find proteins for Q7A0I6 (Staphylococcus aureus (strain MW2))
Explore Q7A0I6 
Go to UniProtKB:  Q7A0I6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7A0I6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M0E
Query on M0E

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
MOENOMYCIN
C69 H106 N5 O34 P
NXPRJQIAIORCGO-ZLPAOQQDSA-N
 Ligand Interaction
1QW
Query on 1QW

Download Ideal Coordinates CCD File 
O [auth A](2R)-2,3-dihydroxypropyl dodecanoate
C15 H30 O4
ARIWANIATODDMH-CQSZACIVSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.422α = 90
b = 114.422β = 90
c = 128.844γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references