6WMV

Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii with evidence of substrate binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Characterization of Phosphatidylinositol-Phosphate Biosynthesis in Mycobacteria.

Belcher Dufrisne, M.Jorge, C.D.Timoteo, C.G.Petrou, V.I.Ashraf, K.U.Banerjee, S.Clarke, O.B.Santos, H.Mancia, F.

(2020) J Mol Biol 432: 5137-5151

  • DOI: https://doi.org/10.1016/j.jmb.2020.04.028
  • Primary Citation of Related Structures:  
    6WM5, 6WMV

  • PubMed Abstract: 

    In mycobacteria, phosphatidylinositol (PI) acts as a common lipid anchor for key components of the cell wall, including the glycolipids phosphatidylinositol mannoside, lipomannan, and lipoarabinomannan. Glycolipids in Mycobacterium tuberculosis, the causative agent of tuberculosis, are important virulence factors that modulate the host immune response. The identity-defining step in PI biosynthesis in prokaryotes, unique to mycobacteria and few other bacterial species, is the reaction between cytidine diphosphate-diacylglycerol and inositol-phosphate to yield phosphatidylinositol-phosphate, the immediate precursor to PI. This reaction is catalyzed by the cytidine diphosphate-alcohol phosphotransferase phosphatidylinositol-phosphate synthase (PIPS), an essential enzyme for mycobacterial viability. Here we present structures of PIPS from Mycobacterium kansasii with and without evidence of donor and acceptor substrate binding obtained using a crystal engineering approach. PIPS from Mycobacterium kansasii is 86% identical to the ortholog from M. tuberculosis and catalytically active. Functional experiments guided by our structural results allowed us to further characterize the molecular determinants of substrate specificity and catalysis in a new mycobacterial species. This work provides a framework to strengthen our understanding of phosphatidylinositol-phosphate biosynthesis in the context of mycobacterial pathogens.


  • Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusionA,
B [auth C]
370Archaeoglobus fulgidusMycobacterium kansasii ATCC 12478
This entity is chimeric
Mutation(s): 3 
Gene Names: XD40_0003XD48_0797MKAN_26045
EC: 2.7.8
Membrane Entity: Yes 
UniProt
Find proteins for U5WZP7 (Mycobacterium kansasii ATCC 12478)
Explore U5WZP7 
Go to UniProtKB:  U5WZP7
Find proteins for O27985 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O27985 
Go to UniProtKB:  O27985
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsU5WZP7O27985
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
U [auth C]
V [auth C]
I [auth A],
J [auth A],
K [auth A],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
C5P (Subject of Investigation/LOI)
Query on C5P

Download Ideal Coordinates CCD File 
Q [auth C]CYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O8 P
IERHLVCPSMICTF-XVFCMESISA-N
LIP (Subject of Investigation/LOI)
Query on LIP

Download Ideal Coordinates CCD File 
C [auth A]L-MYO-INOSITOL-1-PHOSPHATE
C6 H11 O9 P
INAPMGSXUVUWAF-PTQMNWPWSA-L
8K6
Query on 8K6

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L [auth A]
M [auth A]
N [auth A]
O [auth A]
Y [auth C]
L [auth A],
M [auth A],
N [auth A],
O [auth A],
Y [auth C],
Z [auth C]
Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
TCE
Query on TCE

Download Ideal Coordinates CCD File 
G [auth A]3,3',3''-phosphanetriyltripropanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
1PE
Query on 1PE

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H [auth A],
T [auth C]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
FLC
Query on FLC

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R [auth C]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL
Query on GOL

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AA [auth C],
BA [auth C],
P [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

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D [auth A],
E [auth A],
F [auth A],
S [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.089α = 90
b = 60.857β = 90.74
c = 85.417γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling
PARROTphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI119672
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM132120
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM111980

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description