2VG0

Rv1086 citronellyl pyrophosphate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The structural basis of chain length control in Rv1086.

Wang, W.Dong, C.McNeil, M.Kaur, D.Mahapatra, S.Crick, D.C.Naismith, J.H.

(2008) J Mol Biol 381: 129-140

  • DOI: 10.1016/j.jmb.2008.05.060
  • Primary Citation of Related Structures:  
    2VG3, 2VG4, 2VFW, 2VG0, 2VG1, 2VG2

  • PubMed Abstract: 
  • In Mycobacterium tuberculosis, two related Z-prenyl diphosphate synthases, E,Z-farnesyl diphosphate synthase (Rv1086) and decaprenyl diphosphate synthase (Rv2361c), work in series to synthesize decaprenyl phosphate (C(50)) from isopentenyl diphosphat ...

    In Mycobacterium tuberculosis, two related Z-prenyl diphosphate synthases, E,Z-farnesyl diphosphate synthase (Rv1086) and decaprenyl diphosphate synthase (Rv2361c), work in series to synthesize decaprenyl phosphate (C(50)) from isopentenyl diphosphate and E-geranyl diphosphate. Decaprenyl phosphate plays a central role in the biosynthesis of essential mycobacterial cell wall components, such as the mycolyl-arabinogalactan-peptidoglycan complex and lipoarabinomannan; thus, its synthesis has attracted considerable interest as a potential therapeutic target. Rv1086 is a unique prenyl diphosphate synthase in that it adds only one isoprene unit to geranyl diphosphate, generating the 15-carbon product (E,Z-farnesyl diphosphate). Rv2361c then adds a further seven isoprene units to E,Z-farnesyl diphosphate in a processive manner to generate the 50-carbon prenyl diphosphate, which is then dephosphorylated to generate a carrier for activated sugars. The molecular basis for chain-length discrimination by Rv1086 during synthesis is unknown. We also report the structure of apo Rv1086 with citronellyl diphosphate bound and with the product mimic E,E-farnesyl diphosphate bound. We report the structures of Rv2361c in the apo form, with isopentenyl diphosphate bound and with a substrate analogue, citronellyl diphosphate. The structures confirm the enzymes are very closely related. Detailed comparison reveals structural differences that account for chain-length control in Rv1086. We have tested this hypothesis and have identified a double mutant of Rv1086 that makes a range of longer lipid chains.


    Organizational Affiliation

    Centre for Biomolecular Science, The University, St. Andrews, Scotland KY16 9RH, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SHORT-CHAIN Z-ISOPRENYL DIPHOSPHATE SYNTHETASEAB227Mycobacterium tuberculosisMutation(s): 0 
EC: 2.5.1.68
Find proteins for P9WFF5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFF5 
Go to UniProtKB:  P9WFF5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GPP
Query on GPP

Download CCD File 
A, B
GERANYL DIPHOSPHATE
C10 H20 O7 P2
GVVPGTZRZFNKDS-JXMROGBWSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.517α = 90
b = 73.541β = 90
c = 102.561γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata reduction
MOSFLMdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-12-13
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2018-02-07
    Changes: Database references