7ETY | pdb_00007ety

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

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Ligand Structure Quality Assessment 

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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 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.


Macromolecules
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: 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
Expand
  • 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]
1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE
C12 H18 N O9 P
AULMJMUNCOBRHC-MXWKQRLJSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
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
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 137Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary