4Q7C

Structure of AF2299, a CDP-alcohol phosphotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.102 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for catalysis in a CDP-alcohol phosphotransferase.

Sciara, G.Clarke, O.B.Tomasek, D.Kloss, B.Tabuso, S.Byfield, R.Cohn, R.Banerjee, S.Rajashankar, K.R.Slavkovic, V.Graziano, J.H.Shapiro, L.Mancia, F.

(2014) Nat Commun 5: 4068-4068

  • DOI: 10.1038/ncomms5068
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The CDP-alcohol phosphotransferase (CDP-AP) family of integral membrane enzymes catalyses the transfer of a substituted phosphate group from a CDP-linked donor to an alcohol acceptor. This is an essential reaction for phospholipid biosynthesis across ...

    The CDP-alcohol phosphotransferase (CDP-AP) family of integral membrane enzymes catalyses the transfer of a substituted phosphate group from a CDP-linked donor to an alcohol acceptor. This is an essential reaction for phospholipid biosynthesis across all kingdoms of life, and it is catalysed solely by CDP-APs. Here we report the 2.0 Å resolution crystal structure of a representative CDP-AP from Archaeoglobus fulgidus. The enzyme (AF2299) is a homodimer, with each protomer consisting of six transmembrane helices and an N-terminal cytosolic domain. A polar cavity within the membrane accommodates the active site, lined with the residues from an absolutely conserved CDP-AP signature motif (D(1)xxD(2)G(1)xxAR...G(2)xxxD(3)xxxD(4)). Structures in the apo, CMP-bound, CDP-bound and CDP-glycerol-bound states define functional roles for each of these eight conserved residues and allow us to propose a sequential, base-catalysed mechanism universal for CDP-APs, in which the fourth aspartate (D4) acts as the catalytic base.


    Organizational Affiliation

    1] Department of Physiology and Cellular Biophysics, Columbia University, New York, New York 10032, USA [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AF2299, a CDP-alcohol phosphotransferase
A, B
372Archaeoglobus 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: 
AF2299 CDP-alcohol phosphotransferase w. bound CMP
Find proteins for O27985 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O27985
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TLA
Query on TLA

Download SDF File 
Download CCD File 
A, B
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
MPG
Query on MPG

Download SDF File 
Download CCD File 
A, B
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
 Ligand Interaction
C2G
Query on C2G

Download SDF File 
Download CCD File 
A, B
[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
CYTIDINE 5'-DIPHOSPHOGLYCEROL
C12 H21 N3 O13 P2
HHPOUCCVONEPRK-CNYIRLTGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.102 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.417α = 90.00
b = 90.852β = 92.21
c = 106.611γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references