4J9J | pdb_00004j9j

Structure of designed HisF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.297 (Depositor), 0.296 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Establishing catalytic activity on an artificial ( beta alpha )8-barrel protein designed from identical half-barrels.

Sperl, J.M.Rohweder, B.Rajendran, C.Sterner, R.

(2013) FEBS Lett 587: 2798-2805

  • DOI: https://doi.org/10.1016/j.febslet.2013.06.022
  • Primary Citation Related Structures: 
    4J9J

  • PubMed Abstract: 

    It has been postulated that the ubiquitous (βα)8-barrel enzyme fold has evolved by duplication and fusion of an ancestral (βα)4-half-barrel. We have previously reconstructed this process in the laboratory by fusing two copies of the C-terminal half-barrel HisF-C of imidazole glycerol phosphate synthase (HisF). The resulting construct HisF-CC was stepwise stabilized to Sym1 and Sym2, which are extremely robust but catalytically inert proteins. Here, we report on the generation of a circular permutant of Sym2 and the establishment of a sugar isomerization reaction on its scaffold. Our results demonstrate that duplication and mutagenesis of (βα)4-half-barrels can readily lead to a stable and catalytically active (βα)8-barrel enzyme.


  • Organizational Affiliation
    • Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 26.33 kDa 
  • Atom Count: 1,862 
  • Modeled Residue Count: 227 
  • Deposited Residue Count: 246 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Imidazole glycerol phosphate synthase subunit HisF246Thermotoga maritima MSB8Mutation(s): 6 
Gene Names: hisFTM_1036
EC: 4.1.3 (PDB Primary Data), 4.3.2.10 (UniProt)
UniProt
Find proteins for Q9X0C6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0C6 
Go to UniProtKB:  Q9X0C6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0C6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.297 (Depositor), 0.296 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.212α = 90
b = 63.142β = 99.03
c = 56.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Source and taxonomy
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description