6H5E

Crystal Structure of the GatD/MurT Enzyme Complex from Staphylococcus aureus with bound AMPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus.

Noldeke, E.R.Muckenfuss, L.M.Niemann, V.Muller, A.Stork, E.Zocher, G.Schneider, T.Stehle, T.

(2018) Sci Rep 8: 12953-12953

  • DOI: https://doi.org/10.1038/s41598-018-31098-x
  • Primary Citation of Related Structures:  
    6GS2, 6H5E

  • PubMed Abstract: 

    The peptidoglycan of Staphylococcus aureus is highly amidated. Amidation of α-D-isoglutamic acid in position 2 of the stem peptide plays a decisive role in the polymerization of cell wall building blocks. S. aureus mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin, indicating that targeting the amidation reaction could be a useful strategy to combat this pathogen. The enzyme complex that catalyzes the formation of α-D-isoglutamine in the Lipid II stem peptide was identified recently and shown to consist of two subunits, the glutamine amidotransferase-like protein GatD and the Mur ligase homolog MurT. We have solved the crystal structure of the GatD/MurT complex at high resolution, revealing an open, boomerang-shaped conformation in which GatD is docked onto one end of MurT. Putative active site residues cluster at the interface between GatD and MurT and are contributed by both proteins, thus explaining the requirement for the assembled complex to carry out the reaction. Site-directed mutagenesis experiments confirm the validity of the observed interactions. Small-angle X-ray scattering data show that the complex has a similar conformation in solution, although some movement at domain interfaces can occur, allowing the two proteins to approach each other during catalysis. Several other Gram-positive pathogens, including Streptococcus pneumoniae, Clostridium perfringens and Mycobacterium tuberculosis have homologous enzyme complexes. Combined with established biochemical assays, the structure of the GatD/MurT complex provides a solid basis for inhibitor screening in S. aureus and other pathogens.


  • Organizational Affiliation

    Interfaculty Institute of Biochemistry, University of Tübingen, D-72076, Tübingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SA1707 protein
A, C
251Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: SA1707
UniProt
Find proteins for A0A0H3JN63 (Staphylococcus aureus (strain N315))
Explore A0A0H3JN63 
Go to UniProtKB:  A0A0H3JN63
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JN63
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF1727 domain-containing protein
B, D
437Staphylococcus aureusMutation(s): 0 
Gene Names: BTN44_02275C3B39_12565EP54_01845EQ90_00760HMPREF3211_01062
UniProt
Find proteins for A0A0H3JUU7 (Staphylococcus aureus (strain N315))
Explore A0A0H3JUU7 
Go to UniProtKB:  A0A0H3JUU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JUU7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
F [auth B],
N [auth D]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
144
Query on 144

Download Ideal Coordinates CCD File 
H [auth C]TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
C4 H12 N O3
DRDCQJADRSJFFD-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth C],
R [auth D],
S [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth C],
J [auth C],
K [auth C],
P [auth D],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth B],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.72α = 90
b = 109.74β = 90
c = 123.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyDFG-SFB-766
German Research FoundationGermanyDFG-SFB-TR34

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2018-09-26
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description