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 

wwPDB Validation 3D Report Full Report



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: 10.1107/S2053230X19001213
  • Structures With Same Primary Citation

  • 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 int ...

    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

    State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 43420, People's Republic of China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Decaprenyl diphosphate synthaseA, B296Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: uppSRv2361cMTCY27.19
EC: 2.5.1.86 (PDB Primary Data), 2.5.1.87 (PDB Primary Data)
Find proteins for P9WFF7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFF7 
Go to UniProtKB:  P9WFF7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GST
Query on GST

Download CCD File 
A, B
GERANYL S-THIOLODIPHOSPHATE
C10 H20 O6 P2 S
AKIXWSDUEPPMKM-JXMROGBWSA-N
 Ligand Interaction
ISY
Query on ISY

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B
3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid
C5 H12 O6 P2 S
YLTQZUVQWVAPNP-UHFFFAOYSA-N
 Ligand Interaction
DTT
Query on DTT

Download CCD File 
B
2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
GOL
Query on GOL

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B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

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B
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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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Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release