Anthranilate phosphoribosyltransferase from Thermococcus kodakaraensis

Experimental Data Snapshot

  • Resolution: 2.42 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure.

Perveen, S.Rashid, N.Tang, X.F.Imanaka, T.Papageorgiou, A.C.

(2017) FEBS Open Bio 7: 1217-1230

  • DOI: https://doi.org/10.1002/2211-5463.12264
  • Primary Citation of Related Structures:  
    5NOE, 5NOF

  • PubMed Abstract: 

    Anthranilate phosphoribosyltransferase (TrpD) is involved in tryptophan biosynthesis, catalyzing the transfer of a phosphoribosyl group to anthranilate, leading to the generation of phosphoribosyl anthranilate. TrpD belongs to the phosphoribosyltransferase (PRT) superfamily and is the only member of the structural class IV. X-ray structures of TrpD from seven species have been solved to date. Here, functional and structural characterization of a recombinant TrpD from hyperthermophilic archaeon Thermococcus kodakarensis KOD1 ( Tk TrpD) was carried out. Contrary to previously characterized Mg 2+ -dependent TrpD enzymes, Tk TrpD was found to have a unique divalent cation dependency characterized by maximum activity in the presence of Zn 2+ (1580 μmol·min -1 ·mg -1 , the highest reported for any TrpD) followed by Ca 2+ (948 μmol·min -1 ·mg -1 ) and Mg 2+ (711 μmol·min -1 ·mg -1 ). Tk TrpD displayed an unusually low thermostability compared to other previously characterized proteins from T. kodakarensis KOD1. The crystal structure of Tk TrpD was determined in free form and in the presence of Zn 2+ to 1.9 and 2.4 Å resolutions, respectively. Tk TrpD structure displayed the typical PRT fold similar to other class IV PRTs, with a small N-terminal α-helical domain and a larger C-terminal α/β domain. Electron densities for Zn 2+ were identified at the expected zinc-binding motif, DE(217-218), of the enzyme in each subunit of the dimer. Two additional Zn 2+ were found at a new dimer interface formed in the presence of Zn 2+ . A fifth Zn 2+ was found bound to Glu118 at crystal lattice contacts and a sixth one was ligated with Glu235. Based on the Tk TrpD-Zn 2+ structure, it is suggested that the formation of a new dimer may be responsible for the higher enzyme activity of Tk TrpD in the presence of Zn 2+ ions.

  • Organizational Affiliation

    School of Biological Sciences University of the Punjab Lahore Pakistan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anthranilate phosphoribosyltransferase
A, B
325Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: trpDTK0253
Find proteins for Q9YGB4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q9YGB4 
Go to UniProtKB:  Q9YGB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YGB4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B]
Query on CL

Download Ideal Coordinates CCD File 
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.605α = 90
b = 81.389β = 90
c = 179.392γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-01-17
    Changes: Refinement description