6H59 | pdb_00006h59

Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) with CDP-DAG bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.229 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure ofMycobacterium tuberculosisphosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis.

Grave, K.Bennett, M.D.Hogbom, M.

(2019) Commun Biol 2: 175-175

  • DOI: https://doi.org/10.1038/s42003-019-0427-1
  • Primary Citation Related Structures: 
    6H53, 6H59, 6H5A

  • PubMed Abstract: 

    Tuberculosis causes over one million yearly deaths, and drug resistance is rapidly developing. Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) is an integral membrane enzyme involved in biosynthesis of inositol-derived phospholipids required for formation of the mycobacterial cell wall, and a potential drug target. Here we present three crystal structures of M. tuberculosis PgsA1: in absence of substrates (2.9 Å), in complex with Mn 2+ and citrate (1.9 Å), and with the CDP-DAG substrate (1.8 Å). The structures reveal atomic details of substrate binding as well as coordination and dynamics of the catalytic metal site. In addition, molecular docking supported by mutagenesis indicate a binding mode for the second substrate, D- myo -inositol-3-phosphate. Together, the data describe the structural basis for M. tuberculosis phosphatidylinositol phosphate synthesis and suggest a refined general catalytic mechanism-including a substrate-induced carboxylate shift-for Class I CDP-alcohol phosphotransferases, enzymes essential for phospholipid biosynthesis in all domains of life.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16 C, SE-106 91 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 54.34 kDa 
  • Atom Count: 3,429 
  • Modeled Residue Count: 395 
  • Deposited Residue Count: 434 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CDP-diacylglycerol--inositol 3-phosphatidyltransferase
A, B
217Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pgsA1Rv2612c
EC: 2.7.8.11 (PDB Primary Data), 2.7.8 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P9WPG7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPG7 
Go to UniProtKB:  P9WPG7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WPG7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FQT

Query on FQT



Download:Ideal Coordinates CCD File
AA [auth B],
K [auth A]
[(2~{S})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-1,4-dihydropyrimidin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-hexanoyloxy-propyl] hexanoate
C24 H43 N3 O15 P2
ZCBKOYRYPJUKTK-PFMQYRJWSA-N
OLB

Query on OLB



Download:Ideal Coordinates CCD File
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
HA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
GA [auth B]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
J [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
T [auth A],
U [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
V [auth B],
W [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.229 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.986α = 90
b = 115.08β = 90
c = 45.472γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description