5H0I

Name to be released when published


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Engineering a Catalytically Efficient Recombinant Protein Ligase

Yang, R.Wong, Y.H.Nguyen, G.K.T.Tam, J.P.Lescar, J.Wu, B.

(2017) J. Am. Chem. Soc. 139: 5351-5358

  • DOI: 10.1021/jacs.6b12637

  • PubMed Abstract: 
  • Breaking and forming peptidyl bonds are fundamental biochemical reactions in protein chemistry. Unlike proteases that are abundantly available, fast-acting ligases are rare. OaAEP1 is an enzyme isolated from the cyclotide-producing plant oldenlandia ...

    Breaking and forming peptidyl bonds are fundamental biochemical reactions in protein chemistry. Unlike proteases that are abundantly available, fast-acting ligases are rare. OaAEP1 is an enzyme isolated from the cyclotide-producing plant oldenlandia affinis that displayed weak peptide cyclase activity, despite having a similar structural fold with other asparaginyl endopeptidases (AEP). Here we report the first atomic structure of OaAEP1, at a resolution of 2.56 Å, in its preactivation form. Our structure and biochemical analysis of this enzyme reveals its activation mechanism as well as structural features important for its ligation activity. Importantly, through structure-based mutagenesis of OaAEP1, we obtained an ultrafast variant having hundreds of times faster catalytic kinetics, capable of ligating well-folded protein substrates using only a submicromolar concentration of enzyme. In contrast, the protein-protein ligation activity in the original wild-type OaAEP1 enzyme described previously is extremely weak. Thus, the structure-based engineering of OaAEP1 described here provides a unique and novel recombinant tool that can now be used to conduct various protein labeling and modifications that were extremely challenging before.


    Organizational Affiliation

    School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 636921.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Asparaginyl endopeptidase
A, B
448Oldenlandia affinisMutation(s): 0 
EC: 3.4.22.34
Find proteins for A0A0N9JZ32 (Oldenlandia affinis)
Go to UniProtKB:  A0A0N9JZ32
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.730α = 90.00
b = 70.210β = 117.14
c = 118.280γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Nanyang Technological UniversitySingaporeNAP SUG

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references