6VPT

Crystal structure and mechanistic molecular modeling studies of Rv3377c: the Mycobacterium tuberculosis diterpene cyclase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

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Literature

Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c.

Zhang, Y.Prach, L.M.O'Brien, T.E.DiMaio, F.Prigozhin, D.M.Corn, J.E.Alber, T.Siegel, J.B.Tantillo, D.J.

(2020) Biochemistry 59: 4507-4515

  • DOI: https://doi.org/10.1021/acs.biochem.0c00762
  • Primary Citation of Related Structures:  
    6VPT

  • PubMed Abstract: 

    Terpenes make up the largest class of natural products, with extensive chemical and structural diversity. Diterpenes, mostly isolated from plants and rarely prokaryotes, exhibit a variety of important biological activities and valuable applications, including providing antitumor and antibiotic pharmaceuticals. These natural products are constructed by terpene synthases, a class of enzymes that catalyze one of the most complex chemical reactions in biology: converting simple acyclic oligo-isoprenyl diphosphate substrates to complex polycyclic products via carbocation intermediates. Here we obtained the second ever crystal structure of a class II diterpene synthase from bacteria, tuberculosinol pyrophosphate synthase (i.e., Halimadienyl diphosphate synthase, MtHPS, or Rv3377c) from Mycobacterium tuberculosis ( Mtb ). This enzyme transforms ( E,E,E )-geranylgeranyl diphosphate into tuberculosinol pyrophosphate (Halimadienyl diphosphate). Rv3377c is part of the Mtb diterpene pathway along with Rv3378c, which converts tuberculosinol pyrophosphate to 1-tuberculosinyl adenosine (1-TbAd). This pathway was shown to exist only in virulent Mycobacterium species, but not in closely related avirulent species, and was proposed to be involved in phagolysosome maturation arrest. To gain further insight into the reaction pathway and the mechanistically relevant enzyme substrate binding orientation, electronic structure calculation and docking studies of reaction intermediates were carried out. Results reveal a plausible binding mode of the substrate that can provide the information to guide future drug design and anti-infective therapies of this biosynthetic pathway.


  • Organizational Affiliation

    Department of Chemistry, University of California-Davis, Davis, California 95616, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclase501Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ERS023446_02740EZX46_08560FDK60_02635FDK62_05385SAMEA2682864_03253SAMEA2683035_03439
UniProt
Find proteins for O50406 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O50406 
Go to UniProtKB:  O50406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO50406
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.9α = 90
b = 76.428β = 91.64
c = 50.123γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1827246,1805510,1627539,CHE-1565933,CHE-030089
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM076324, P42ES004699

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-02
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description