Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54786.91 
• Atom Count: 3151 
• Residue Count: 479 
• Unique protein chains: 1

4MND

Crystal structure of Archaeoglobus fulgidus IPCT-DIPPS bifunctional membrane protein

• DOI: 10.2210/pdb4MND/pdb

• Classification: TRANSFERASE
• Organism(s): Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
• Expression System: Escherichia coli


• Deposited: 2013-09-10 Released: 2014-07-02 
• Deposition Author(s): Nogly, P., Gushchin, I., Remeeva, A., Esteves, A.M., Ishchenko, A., Ma, P., Grudinin, S., Borges, N., Round, E., Moraes, I., Borshchevskiy, V., Santos, H., Gordeliy, V., Archer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.300 
• R-Value Work: 0.243 

Literature

X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism.

Nogly, P., Gushchin, I., Remeeva, A., Esteves, A.M., Borges, N., Ma, P., Ishchenko, A., Grudinin, S., Round, E., Moraes, I., Borshchevskiy, V., Santos, H., Gordeliy, V., Archer, M.

(2014) Nat Commun 5: 4169-4169

• PubMed: 24942835 
• DOI: 10.1038/ncomms5169


• PubMed Abstract: 
  

Phospholipids have major roles in the structure and function of all cell membranes. Most integral membrane proteins from the large CDP-alcohol phosphatidyltransferase family are involved in phospholipid biosynthesis across the three domains of life. They share a conserved sequence pattern and catalyse the displacement of CMP from a CDP-alcohol by a second alcohol. Here we report the crystal structure of a bifunctional enzyme comprising a cytoplasmic nucleotidyltransferase domain (IPCT) fused with a membrane CDP-alcohol phosphotransferase domain (DIPPS) at 2.65 Å resolution. The bifunctional protein dimerizes through the DIPPS domains, each comprising six transmembrane α-helices. The active site cavity is hydrophilic and widely open to the cytoplasm with a magnesium ion surrounded by four highly conserved aspartate residues from helices TM2 and TM3. We show that magnesium is essential for the enzymatic activity and is involved in catalysis. Substrates docking is validated by mutagenesis studies, and a structure-based catalytic mechanism is proposed.

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Organizational Affiliation: 

1] Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa (ITQB-UNL), Av. República, EAN, 2780-157 Oeiras, Portugal [2].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CTP L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase	A	479	Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)	Mutation(s): 0
Membrane protein mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  CDP-Alcohol Phosphotransferases	Protein:  CDP-alcohol phosphotransferase domain (DIPPS) with fused nucleotidyltransferase domain
Find proteins for O29976 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)) Go to UniProtKB:  O29976

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
LFA	A	EICOSANE LIPID FRAGMENT C20 H42 CBFCDTFDPHXCNY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.300 
• R-Value Work: 0.243 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 41.369	α = 90.00
b = 107.584	β = 90.00
c = 123.953	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-10 
• Released Date: 2014-07-02 
• Deposition Author(s): Nogly, P., Gushchin, I., Remeeva, A., Esteves, A.M., Ishchenko, A., Ma, P., Grudinin, S., Borges, N., Round, E., Moraes, I., Borshchevskiy, V., Santos, H., Gordeliy, V., Archer, M.

Revision History 

• Version 1.0: 2014-07-02
  Type: Initial release