4EWN

Structure of HisF-D130V+D176V with bound rCdRP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4EWN

  • 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 acid and base, respectively ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Imidazole glycerol phosphate synthase subunit HisFA [auth D]253Thermotoga maritimaMutation(s): 2 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0VR
Query on 0VR

Download Ideal Coordinates CCD File 
B [auth D]1-(O-carboxy-phenylamino)-1-deoxy-D-ribulose-5-phosphate
C12 H18 N O9 P
AULMJMUNCOBRHC-AXFHLTTASA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0VR Binding MOAD:  4EWN Kd: 200 (nM) from 1 assay(s)
PDBBind:  4EWN Kd: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.205 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.654α = 90
b = 112.517β = 90
c = 163.402γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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