Structure of sortase E from Streptomyces avermitilis

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structure and specificity of a new class of Ca2+-independent housekeeping sortase from Streptomyces avermitilis provide insights into its non-canonical substrate preference.

Das, S.Pawale, V.S.Dadireddy, V.Singh, A.K.Ramakumar, S.Roy, R.P.

(2017) J Biol Chem 292: 7244-7257

  • DOI: https://doi.org/10.1074/jbc.M117.782037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Surface proteins in Gram-positive bacteria are incorporated into the cell wall through a peptide ligation reaction catalyzed by transpeptidase sortase. Six main classes (A-F) of sortase have been identified of which class A sortase is meant for housekeeping functions. The prototypic housekeeping sortase A (SaSrtA) from Staphylococcus aureus cleaves LP X TG-containing proteins at the scissile T-G peptide bond and ligates protein-LP X T to the terminal Gly residue of the nascent cross-bridge of peptidoglycan lipid II precursor. Sortase-mediated ligation ("sortagging") of LP X TG-containing substrates and Gly-terminated nucleophiles occurs in vitro as well as in cellulo in the presence of Ca 2+ and has been applied extensively for protein conjugations. Although the majority of applications emanate from SaSrtA, low catalytic efficiency, LP X TG specificity restriction, and Ca 2+ requirement (particularly for in cellulo applications) remain a drawback. Given that Gram-positive bacteria genomes encode a variety of sortases, natural sortase mining can be a viable complementary approach akin to engineering of wild-type SaSrtA. Here, we describe the structure and specificity of a new class E sortase (SavSrtE) annotated to perform housekeeping roles in Streptomyces avermitilis Biochemical experiments define the attributes of an optimum peptide substrate, demonstrate Ca 2+ -independent activity, and provide insights about contrasting functional characteristics of SavSrtE and SaSrtA. Crystal structure, substrate docking, and mutagenesis experiments have identified a critical residue that dictates the preference for a non-canonical LA X TG recognition motif over LP X TG. These results have implications for rational tailoring of substrate tolerance in sortases. Besides, Ca 2+ -independent orthogonal specificity of SavSrtE is likely to expand the sortagging toolkit.

  • Organizational Affiliation

    From the Department of Physics, Indian Institute of Science, Bangalore 560012, and.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
sortase201Streptomyces avermitilis MA-4680 = NBRC 14893Mutation(s): 0 
Gene Names: SAVERM_4333
Find proteins for Q82FC3 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680))
Explore Q82FC3 
Go to UniProtKB:  Q82FC3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82FC3
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CME
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.84α = 90
b = 85.84β = 90
c = 48.2γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description