Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 136.48 kDa 
• Atom Count: 10271 
• Residue Count: 1139 
• Unique protein chains: 1

3WQL

Crystal structure of Rv3378c with Mg2+ and PPi

• DOI: 10.2210/pdb3WQL/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-01-28 Released: 2014-02-19 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.239 
• R-Value Work: 0.198 

Literature

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

• PubMed: 24475925 
• DOI: 10.1021/ja413127v
• Primary Citation of Related Structures:  
  4KT8, 3WQK, 3WQL, 3WQM, 3WQN, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diterpene synthase	A, B, C, D	296	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv3378c, MT3488 EC: 3.1.7.9 (PDB Primary Data), 3.1.7.8 (PDB Primary Data), 2.5.1 (UniProt)
Find proteins for P9WJ61 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJ61  Go to UniProtKB:  P9WJ61

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A, B, C, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 208.42	α = 90
b = 56.525	β = 90.28
c = 114.435	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-28 
• Released Date: 2014-02-19 
Deposition Author(s): 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.

Revision History 

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references