4ONC

Crystal Structure of Mycobacterium Tuberculosis Decaprenyl Diphosphate Synthase in Complex with BPH-640

• PDB DOI: https://doi.org/10.2210/pdb4ONC/pdb

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


• Deposited: 2014-01-28 Released: 2014-04-02 
• Deposition Author(s): Feng, X., Chan, H.C., Ko, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.198 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Starting Model: experimental

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: 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 65.76 kDa 
• Atom Count: 4,991 
• Modelled Residue Count: 559 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decaprenyl diphosphate synthase	A, B	284	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv2361c EC: 2.5.1.86 (PDB Primary Data), 2.5.1.87 (PDB Primary Data)
UniProt
Find proteins for P9WFF7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFF7  Go to UniProtKB:  P9WFF7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
40B	C [auth A], D [auth B]	[hydroxy(1,1':3',1''-terphenyl-3-yl)methanediyl]bis(phosphonic acid) C19 H18 O7 P2 QLUPVXJJKKYIHH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
40B	BindingDB:  4ONC	IC50: min: 410, max: 610 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.198 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.809	α = 90
b = 89.167	β = 90
c = 93.88	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Feng, X., Chan, H.C., Ko, T.P.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description