Crystal structure of bifunctional indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC) from Corynebacterium glutamicum in complex with reduced 1-(O-carboxyphenylamino)-1-deoxyribulose 5-phosphate (rCdRP)

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 

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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 of 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan biosynthesis protein TrpCF
A, B
482Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: trpCtrpCFCgl3033cg3362
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P06560 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore P06560 
Go to UniProtKB:  P06560
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06560
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
137 (Subject of Investigation/LOI)
Query on 137

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
L [auth B],
M [auth B]
C12 H18 N O9 P
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.74α = 90
b = 98.163β = 90
c = 116.124γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release