4JD0 | pdb_00004jd0

Structure of the inositol-1-phosphate CTP transferase from T. maritima.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.166 (Depositor), 0.166 (DCC) 
  • R-Value Work: 
    0.111 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 
    0.114 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure of the inositol-1-phosphate cytidylyltransferase from Thermotoga maritima.

Kurnasov, O.V.Luk, H.J.Roberts, M.F.Stec, B.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1808-1817

  • DOI: https://doi.org/10.1107/S0907444913015278
  • Primary Citation Related Structures: 
    4JD0

  • PubMed Abstract: 

    The unique steps in the synthesis of an unusual osmolyte in hyperthermophiles, di-myo-inositol-1,1'-phosphate (DIP), involve the production of CDP-inositol and its condensation with an inositol-1-phosphate molecule to form phosphorylated DIP. While many organisms fuse both activities into a single enzyme, the two are separate in Thermotoga maritima. The crystal structure of the T. maritima inositol-1-phosphate cytidylyltransferase, which as a soluble protein may transiently associate with its membrane-embedded partner phospho-DIP synthase (P-DIPS), has now been obtained. The structure shows a conserved motif of sugar nucleotide transferases (COG1213) with a structurally reinforced C-terminal Cys bonded to the core of the protein. A bound arsenosugar identifies the location of the active site for inositol 1-phosphate. Based on homologous structures from several species and the identification of the crucial conserved aspartate residue, a catalytic mechanism for this enzyme is proposed as well as a mode for its association with P-DIPS. This structure imposes constraints on the mode of association, communication and temperature activation of two separate enzymes in T. maritima. For the first time, a working model for the membrane-bound P-DIPS unit has been constructed. This sheds light on the functioning of the phosphatidylserine and phosphatidylinositol synthases involved in many physiological processes that are homologous to P-DIPS. This work provides fresh insights into the synthesis of the unusual thermoprotective compound DIP in hyperthermophiles.


  • Organizational Affiliation
    • Sanford-Burnham Institute for Medical Research, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 29.35 kDa 
  • Atom Count: 2,419 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 251 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleotidyl transferase251Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: ThemaDRAFT_0946TM1418A

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1KH

Query on 1KH



Download:Ideal Coordinates CCD File
B [auth A]arsenoribose
C5 H13 As O8
MSQKZAOQSOMILW-FLRLBIABSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
D [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
D [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
P [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.166 (Depositor), 0.166 (DCC) 
  • R-Value Work:  0.111 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 0.114 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.09α = 90
b = 133.09β = 90
c = 43.365γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2013-09-18 
  • Deposition Author(s): Stec, B.

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-27
    Changes: Structure summary