6FTB | pdb_00006ftb

Staphylococcus aureus monofunctional glycosyltransferase in complex with moenomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.237 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.tcsw.2018.06.002
  • Primary Citation 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). 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.


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

Macromolecule Content 

  • Total Structure Weight: 30.09 kDa 
  • Atom Count: 2,105 
  • Modeled Residue Count: 210 
  • Deposited Residue Count: 210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Monofunctional glycosyltransferase210Staphylococcus aureus MW2Mutation(s): 0 
Gene Names: mgtMW1814
EC: 2.4.1.129 (PDB Primary Data), 2.4.99.28 (UniProt)
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / 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
1QW

Query on 1QW



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

Query on PO4



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.237 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description