7REP

Crystal structure of an engineered variant of single-chain Penicillin G Acylase from Kluyvera cryocrescens (A1-Ac Rd3CHis)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

A chemoenzymatic strategy for site-selective functionalization of native peptides and proteins.

Fryszkowska, A.An, C.Alvizo, O.Banerjee, G.Canada, K.A.Cao, Y.DeMong, D.Devine, P.N.Duan, D.Elgart, D.M.Farasat, I.Gauthier, D.R.Guidry, E.N.Jia, X.Kong, J.Kruse, N.Lexa, K.W.Makarov, A.A.Mann, B.F.Milczek, E.M.Mitchell, V.Nazor, J.Neri, C.Orr, R.K.Orth, P.Phillips, E.M.Riggins, J.N.Schafer, W.A.Silverman, S.M.Strulson, C.A.Subramanian, N.Voladri, R.Yang, H.Yang, J.Yi, X.Zhang, X.Zhong, W.

(2022) Science 376: 1321-1327

  • DOI: https://doi.org/10.1126/science.abn2009
  • Primary Citation of Related Structures:  
    7REO, 7REP

  • PubMed Abstract: 

    The emergence of new therapeutic modalities requires complementary tools for their efficient syntheses. Availability of methodologies for site-selective modification of biomolecules remains a long-standing challenge, given the inherent complexity and the presence of repeating residues that bear functional groups with similar reactivity profiles. We describe a bioconjugation strategy for modification of native peptides relying on high site selectivity conveyed by enzymes. We engineered penicillin G acylases to distinguish among free amino moieties of insulin (two at amino termini and an internal lysine) and manipulate cleavable phenylacetamide groups in a programmable manner to form protected insulin derivatives. This enables selective and specific chemical ligation to synthesize homogeneous bioconjugates, improving yield and purity compared to the existing methods, and generally opens avenues in the functionalization of native proteins to access biological probes or drugs.


  • Organizational Affiliation

    Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin G acylase770Kluyvera cryocrescensMutation(s): 0 
EC: 3.5.1.11
UniProt
Find proteins for P07941 (Kluyvera cryocrescens)
Explore P07941 
Go to UniProtKB:  P07941
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07941
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.7α = 90
b = 102.7β = 90
c = 255.01γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-11-17 
  • Deposition Author(s): Orth, P.

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 1.1: 2022-06-08
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description