Crystal structure of Rv3378c with Mg2+ and PPi

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 

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Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis.

Chan, H.C.Feng, X.Ko, T.P.Huang, C.H.Hu, Y.Zheng, Y.Bogue, S.Nakano, C.Hoshino, T.Zhang, L.Lv, P.Liu, W.Crick, D.C.Liang, P.H.Wang, A.H.Oldfield, E.Guo, R.T.

(2014) J Am Chem Soc 136: 2892-2896

  • DOI: https://doi.org/10.1021/ja413127v
  • Primary Citation of Related Structures:  
    3WQK, 3WQL, 3WQM, 3WQN, 4KT8, 4ONC

  • PubMed Abstract: 

    We have obtained the structure of the bacterial diterpene synthase, tuberculosinol/iso-tuberculosinol synthase (Rv3378c) from Mycobacterium tuberculosis , a target for anti-infective therapies that block virulence factor formation. This phosphatase adopts the same fold as found in the Z- or cis-prenyltransferases. We also obtained structures containing the tuberculosinyl diphosphate substrate together with one bisphosphonate inhibitor-bound structure. These structures together with the results of site-directed mutagenesis suggest an unusual mechanism of action involving two Tyr residues. Given the similarity in local and global structure between Rv3378c and the M. tuberculosis cis-decaprenyl diphosphate synthase (DPPS; Rv2361c), the possibility exists for the development of inhibitors that target not only virulence but also cell wall biosynthesis, based in part on the structures reported here.

  • Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology , Tianjin 300308, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diterpene synthase
A, B, C, D
296Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv3378cMT3488
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P9WJ61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WJ61 
Go to UniProtKB:  P9WJ61
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WJ61
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.42α = 90
b = 56.525β = 90.28
c = 114.435γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description