6YMU

Imidazole Glycerol Phosphate Synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Significance of the Protein Interface Configuration for Allostery in Imidazole Glycerol Phosphate Synthase.

Kneuttinger, A.C.Rajendran, C.Simeth, N.A.Bruckmann, A.Konig, B.Sterner, R.

(2020) Biochemistry 59: 2729-2742

  • DOI: https://doi.org/10.1021/acs.biochem.0c00332
  • Primary Citation of Related Structures:  
    6YMU

  • PubMed Abstract: 

    Imidazole glycerol phosphate synthase (ImGPS) from Thermotoga maritima is a model enzyme for studying allostery. The ImGPS complex consists of the cyclase subunit HisF and the glutaminase subunit HisH whose activity is stimulated by substrate binding to HisF in a V-type manner. To investigate the significance of a putative closing hinge motion at the cyclase:glutaminase interface for HisH activity, we replaced residue W123 in HisH with the light-switchable unnatural amino acid phenylalanine-4'-azobenzene (AzoF). Crystal structure analysis employing angle, buried surface area, and distance measurements showed that incorporation of AzoF at this position causes a closing of the interface by ∼18 ± 3%. This slightly different interface configuration results in a much higher catalytic efficiency in unstimulated HisH due to an elevated turnover number. Moreover, the catalytic efficiency of HisH when stimulated by binding of a substrate to HisF was also significantly increased by AzoF incorporation. This was caused by a K-type stimulation that led to a decrease in the apparent dissociation constant for its substrate, glutamine. In addition, AzoF improved the apparent binding of a substrate analogue at the HisF active site. Remarkably, light-induced isomerization of AzoF considerably enhanced these effects. In conclusion, our findings confirm that signal transduction from HisF to HisH in ImGPS involves the closing of the cyclase:glutaminase subunit interface and that incorporation of AzoF at a hinge position reinforces this catalytically relevant conformational change.


  • Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazole glycerol phosphate synthase subunit HisF
A, C, E
253Thermotoga maritimaMutation(s): 0 
Gene Names: hisFTM_1036
EC: 4.3.2.10
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazole glycerol phosphate synthase subunit HisH
B, D, F
201Thermotoga maritimaMutation(s): 0 
Gene Names: hisHTM_1038
EC: 4.3.2.10 (PDB Primary Data), 3.5.1.2 (PDB Primary Data)
UniProt
Find proteins for Q9X0C8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X0C8 
Go to UniProtKB:  Q9X0C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X0C8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OZW
Query on OZW
B, D, F
L-PEPTIDE LINKINGC15 H17 N3 O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.417α = 90
b = 85.901β = 108.24
c = 128.745γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySTE891/12-2

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description