4Q7C

Structure of AF2299, a CDP-alcohol phosphotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C2GClick on this verticalbar to view detailsBest fitted MPGClick on this verticalbar to view details

This is version 1.2 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: https://doi.org/10.1038/ncomms5068
  • Primary Citation of Related Structures:  
    4O6M, 4O6N, 4Q7C

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AF2299, a CDP-alcohol phosphotransferase
A, B
372Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: AF2299AF_2299
Membrane Entity: Yes 
UniProt
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 GroupO27985
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2G
Query on C2G

Download Ideal Coordinates CCD File 
J [auth A],
R [auth B]
[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
C12 H21 N3 O13 P2
HHPOUCCVONEPRK-CNYIRLTGSA-N
MPG
Query on MPG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
M [auth B]
[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate
C21 H40 O4
JPJYKWFFJCWMPK-GDCKJWNLSA-N
TLA
Query on TLA

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth B]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.269 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.417α = 90
b = 90.852β = 92.21
c = 106.611γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C2GClick on this verticalbar to view detailsBest fitted MPGClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description