7TJ4

Structure of the S. aureus amidase LytH and activator ActH extracellular domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Metal cofactor stabilization by a partner protein is a widespread strategy employed for amidase activation.

Page, J.E.Skiba, M.A.Do, T.Kruse, A.C.Walker, S.

(2022) Proc Natl Acad Sci U S A 119: e2201141119-e2201141119

  • DOI: https://doi.org/10.1073/pnas.2201141119
  • Primary Citation of Related Structures:  
    7TJ4

  • PubMed Abstract: 

    Construction and remodeling of the bacterial peptidoglycan (PG) cell wall must be carefully coordinated with cell growth and division. Central to cell wall construction are hydrolases that cleave bonds in peptidoglycan. These enzymes also represent potential new antibiotic targets. One such hydrolase, the amidase LytH in Staphylococcus aureus , acts to remove stem peptides from PG, controlling where substrates are available for insertion of new PG strands and consequently regulating cell size. When it is absent, cells grow excessively large and have division defects. For activity, LytH requires a protein partner, ActH, that consists of an intracellular domain, a large rhomboid protease domain, and three extracellular tetratricopeptide repeats (TPRs). Here, we demonstrate that the amidase-activating function of ActH is entirely contained in its extracellular TPRs. We show that ActH binding stabilizes metals in the LytH active site and that LytH metal binding in turn is needed for stable complexation with ActH. We further present a structure of a complex of the extracellular domains of LytH and ActH. Our findings suggest that metal cofactor stabilization is a general strategy used by amidase activators and that ActH houses multiple functions within a single protein.


  • Organizational Affiliation

    Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ActH
A, C
122Staphylococcus aureusMutation(s): 0 
Gene Names: gluPDD547_01635RK64_08320
EC: 3.4.21.105
UniProt
Find proteins for Q2FY25 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FY25 
Go to UniProtKB:  Q2FY25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FY25
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LytH
B, D
176Staphylococcus aureusMutation(s): 0 
Gene Names: lytH
EC: 3.5.1
UniProt
Find proteins for Q2FXU3 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXU3 
Go to UniProtKB:  Q2FXU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FXU3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.6α = 90
b = 71.26β = 90
c = 190.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI139011
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI148752
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM007753
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesF30 AI156972

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description