Structure of glycinamide-RNase-transformylase T from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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Structural characterization of glycinamide-RNase-transformylase T fromMycobacterium tuberculosis.

Chen, C.Liu, Z.Liu, L.Wang, J.Jin, Q.

(2020) Emerg Microbes Infect 9: 58-66

  • DOI: https://doi.org/10.1080/22221751.2019.1707716
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Enzymes from the purine salvage pathway in Mycobacterium tuberculosis ( Mtb ) have been regarded as an attractive target for the development of anti-bacterial drugs. Although this pathway has not been extensively studied in Mtb , it has been identified as essential for growth and survival. Glycinamide-RNase-transformylase T (PurT) is found only in some specific bacteria including Mtb and utilizes ATP-dependent ligation to catalyze the formylation of 5'-phosphoribosyl-glycinamide (GAR) in the third reaction of the de novo purine salvage pathway. In the study, we determined the crystal structure of Mtb PurT at a resolution of 2.79 Å. In contrast to Pyrococcus horikoshii OT3 PurT (phBCCPPurT), Mtb PurT exhibits an "open" conformation, which results in a broader ATP-binding pocket and thus might facilitate the entry and exit of the cofactor. Additionally, active site superposition with E.coli PurT ( Ec PurT) showed that residues involved in the ATP-binding site in Mtb PurT exhibited structural similarity but had notable difference in the GAR-binding site. The loop 383-389 in Mtb PurT was much shorter and shifted 5.7 Å away from the phosphate of the GAR substrate. The different GAR-binding mode might result in a large conformational change in Mtb PurT, and would provide a possible opportunity for anti-TB drug development.

  • Organizational Affiliation

    NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for Tuberculosis Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate-dependent phosphoribosylglycinamide formyltransferase
A, B
420Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: purTRv0389
Find proteins for P95197 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P95197 
Go to UniProtKB:  P95197
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95197
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.79 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.132α = 90
b = 103.132β = 90
c = 148.692γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description