6IME

Rv2361c complex with substrate analogues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase.

Ko, T.-P.Xiao, X.Guo, R.-T.Huang, J.-W.Liu, W.Chen, C.-C.

(2019) Acta Crystallogr F Struct Biol Commun 75: 212-216

  • DOI: https://doi.org/10.1107/S2053230X19001213
  • Primary Citation of Related Structures:  
    6IME

  • PubMed Abstract: 

    Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of ω,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 Å resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis. The ligand-binding mode of GSPP in the other subunit indicates a possible pathway of product translocation from the S2 site to the S1 site, as required for the next step of the reaction. The preferred binding of negatively charged effectors to the S1 site also suggests a promising direction for inhibitor design.


  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Decaprenyl diphosphate synthase
A, B
296Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: uppSRv2361cMTCY27.19
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFF7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GST (Subject of Investigation/LOI)
Query on GST

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
GERANYL S-THIOLODIPHOSPHATE
C10 H20 O6 P2 S
AKIXWSDUEPPMKM-JXMROGBWSA-N
ISY (Subject of Investigation/LOI)
Query on ISY

Download Ideal Coordinates CCD File 
K [auth B]3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid
C5 H12 O6 P2 S
YLTQZUVQWVAPNP-UHFFFAOYSA-N
DTT
Query on DTT

Download Ideal Coordinates CCD File 
G [auth B]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
F [auth B]CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
CL
Query on CL

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E [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.711α = 90
b = 89.12β = 90
c = 94.445γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanAS-KPQ-105-TPP

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description