4EWN

Structure of HisF-D130V+D176V with bound rCdRP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.903 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A sugar isomerization reaction established on various (beta-alpha)8-barrel scaffolds is based on substrate-assisted catalysis

Reisinger, B.Bocola, M.List, F.Claren, J.Rajendran, C.Sterner, R.

(2012) Protein Eng.Des.Sel. 25: 751-760

  • DOI: 10.1093/protein/gzs080

  • PubMed Abstract: 
  • In the course of tryptophan biosynthesis, the isomerization of phosphoribosylanthranilate (PRA) is catalyzed by the (βα)₈-barrel enzyme TrpF. The reaction occurs via a general acid-base mechanism with an aspartate and a cysteine residue acting as aci ...

    In the course of tryptophan biosynthesis, the isomerization of phosphoribosylanthranilate (PRA) is catalyzed by the (βα)₈-barrel enzyme TrpF. The reaction occurs via a general acid-base mechanism with an aspartate and a cysteine residue acting as acid and base, respectively. PRA isomerase activity could be established on two (βα)₈-barrel enzymes involved in histidine biosynthesis, namely HisA and HisF, and on a HisAF chimera, by introducing two aspartate-to-valine substitutions. We have analyzed the reaction mechanism underlying this engineered activity by measuring its pH dependence, solving the crystal structure of a HisF variant with bound product analogue, and applying molecular dynamics simulations and mixed quantum and molecular mechanics calculations. The results suggest that PRA is anchored by the C-terminal phosphate-binding sites of HisA, HisF and HisAF. As a consequence, a conserved aspartate residue, which is equivalent to Cys7 from TrpF, is properly positioned to act as catalytic base. However, no obvious catalytic acid corresponding to Asp126 from TrpF could be identified in the three proteins. Instead, this role appears to be carried out by the carboxylate group of the anthranilate moiety of PRA. Thus, the engineered PRA isomerization activity is based on a reaction mechanism including substrate-assisted catalysis and thus differs substantially from the naturally evolved reaction mechanism used by TrpF.


    Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Imidazole glycerol phosphate synthase subunit HisF
D
253Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: hisF
EC: 4.1.3.-
Find proteins for Q9X0C6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X0C6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0VR
Query on 0VR

Download SDF File 
Download CCD File 
D
1-(O-carboxy-phenylamino)-1-deoxy-D-ribulose-5-phosphate
1-[(2-carboxyphenyl)amino]-1-deoxy-5-O-phosphono-D-ribitol
C12 H18 N O9 P
AULMJMUNCOBRHC-AXFHLTTASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0VRKd: 200 nM BINDINGMOAD
0VRKd: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.903 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 57.654α = 90.00
b = 112.517β = 90.00
c = 163.402γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release