7ETX | pdb_00007etx

Crystal structure of bifunctional indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (TrpC) from corynebacterium glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.252 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

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Literature

Crystal Structure and Functional Characterization of the Bifunctional N -(5'-Phosphoribosyl)anthranilate Isomerase-indole-3-glycerol-phosphate Synthase from Corynebacterium glutamicum

Park, W.Son, H.F.Lee, D.Kim, I.K.Kim, K.J.

(2021) J Agric Food Chem 69: 12485-12493

  • DOI: https://doi.org/10.1021/acs.jafc.1c05132
  • Primary Citation Related Structures: 
    7ETX, 7ETY

  • PubMed Abstract: 

    L-Tryptophan is known as an aromatic amino acid and one of the essential amino acids that must be ingested through various additives or food. TrpCF is a bifunctional enzyme that has indole-glycerol-phosphate synthase (IGPS) and phosphoribosylanthranilate isomerase (PRAI) activity. In this report, we identified the crystal structure of TrpCF from Corynebacterium glutamicum ( Cg TrpCF) and successfully elucidated the active site by attaching rCdRP similar to the substrate and product of the TrpCF reaction. Also, we revealed that Cg TrpCF shows a conformational change at the loops upon substrate binding. We analyzed amino acid sequences of the homologues of Cg TrpCF, and the residues of the substrate-binding site in TrpCF were highly conserved except for some residues. These less conserved residues were replaced by site-directed mutagenesis experiments. Consequently, we obtained the Cg TrpCF P294K (PRAI CD/P294K ) variant that has enhanced activity.


  • Organizational Affiliation
    • School of Life Sciences, BK21 Four KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 51.79 kDa 
  • Atom Count: 3,752 
  • Modeled Residue Count: 472 
  • Deposited Residue Count: 482 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tryptophan biosynthesis protein TrpCF482Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: trpCtrpCFCgl3033cg3362
EC: 4.1.1.48 (PDB Primary Data), 5.3.1.24 (PDB Primary Data)
UniProt
Find proteins for P06560 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore P06560 
Go to UniProtKB:  P06560
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06560
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.681α = 90
b = 90.681β = 90
c = 141.785γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Structure summary