6UEX

Crystal structure of S. aureus LcpA in complex with octaprenyl-pyrophosphate-GlcNAc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystallographic analysis ofStaphylococcus aureusLcpA, the primary wall teichoic acid ligase.

Li, F.K.K.Rosell, F.I.Gale, R.T.Simorre, J.P.Brown, E.D.Strynadka, N.C.J.

(2020) J Biol Chem 295: 2629-2639

  • DOI: https://doi.org/10.1074/jbc.RA119.011469
  • Primary Citation of Related Structures:  
    6UEX, 6UF3, 6UF5, 6UF6

  • PubMed Abstract: 

    Gram-positive bacteria, including major clinical pathogens such as Staphylococcus aureus , are becoming increasingly drug-resistant. Their cell walls are composed of a thick layer of peptidoglycan (PG) modified by the attachment of wall teichoic acid (WTA), an anionic glycopolymer that is linked to pathogenicity and regulation of cell division and PG synthesis. The transfer of WTA from lipid carriers to PG, catalyzed by the LytR-CpsA-Psr (LCP) enzyme family, offers a unique extracellular target for the development of new anti-infective agents. Inhibitors of LCP enzymes have the potential to manage a wide range of bacterial infections because the target enzymes are implicated in the assembly of many other bacterial cell wall polymers, including capsular polysaccharide of streptococcal species and arabinogalactan of mycobacterial species. In this study, we present the first crystal structure of S. aureus LcpA with bound substrate at 1.9 Å resolution and those of Bacillus subtilis LCP enzymes, TagT, TagU, and TagV, in the apo form at 1.6-2.8 Å resolution. The structures of these WTA transferases provide new insight into the binding of lipid-linked WTA and enable assignment of the catalytic roles of conserved active-site residues. Furthermore, we identified potential subsites for binding the saccharide core of PG using computational docking experiments, and multiangle light-scattering experiments disclosed novel oligomeric states of the LCP enzymes. The crystal structures and modeled substrate-bound complexes of the LCP enzymes reported here provide insights into key features linked to substrate binding and catalysis and may aid the structure-guided design of specific LCP inhibitors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada; Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein MsrR273Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: msrRSA1195
UniProt
Find proteins for Q99Q02 (Staphylococcus aureus (strain N315))
Explore Q99Q02 
Go to UniProtKB:  Q99Q02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99Q02
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q5S (Subject of Investigation/LOI)
Query on Q5S

Download Ideal Coordinates CCD File 
B [auth A]2-(acetylamino)-2-deoxy-1-O-[(S)-hydroxy{[(S)-hydroxy{[(2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]oxy}phosphoryl]oxy}phosphoryl]-alpha-D-glucopyranose
C48 H81 N O12 P2
UHEQUFGFBDQLSB-MUZKLJMZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.245α = 90
b = 90.543β = 90
c = 94.753γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Database references
  • Version 1.2: 2020-03-11
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description