4GXP

Chimeric Family 1 beta-glucosidase made with non-contiguous SCHEMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Chimeragenesis of distantly-related proteins by noncontiguous recombination.

Smith, M.A.Romero, P.A.Wu, T.Brustad, E.M.Arnold, F.H.

(2013) Protein Sci. 22: 231-238

  • DOI: 10.1002/pro.2202

  • PubMed Abstract: 
  • We introduce a method for identifying elements of a protein structure that can be shuffled to make chimeric proteins from two or more homologous parents. Formulating recombination as a graph-partitioning problem allows us to identify noncontiguous se ...

    We introduce a method for identifying elements of a protein structure that can be shuffled to make chimeric proteins from two or more homologous parents. Formulating recombination as a graph-partitioning problem allows us to identify noncontiguous segments of the sequence that should be inherited together in the progeny proteins. We demonstrate this noncontiguous recombination approach by constructing a chimera of β-glucosidases from two different kingdoms of life. Although the protein's alpha-beta barrel fold has no obvious subdomains for recombination, noncontiguous SCHEMA recombination generated a functional chimera that takes approximately half its structure from each parent. The X-ray crystal structure shows that the structural blocks that make up the chimera maintain the backbone conformations found in their respective parental structures. Although the chimera has lower β-glucosidase activity than the parent enzymes, the activity was easily recovered by directed evolution. This simple method, which does not rely on detailed atomic models, can be used to design chimeras that take structural, and functional, elements from distantly-related proteins.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-glucosidase Chimeric protein
A, B, C
467Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Hypocrea jecorina
This entity is chimeric
Gene Names: bglA, bgl2
EC: 3.2.1.21
Find proteins for Q08638 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q08638
Find proteins for O93785 (Hypocrea jecorina)
Go to UniProtKB:  O93785
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.239 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 115.377α = 90.00
b = 115.377β = 90.00
c = 282.538γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
XSCALEdata scaling
Blu-Icedata collection
REFMACrefinement
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release
  • Version 1.1: 2013-08-28
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy