3OYR

Crystal structure of polyprenyl synthase from Caulobacter crescentus CB15 complexed with calcium and isoprenyl diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.

Wallrapp, F.H.Pan, J.J.Ramamoorthy, G.Almonacid, D.E.Hillerich, B.S.Seidel, R.Patskovsky, Y.Babbitt, P.C.Almo, S.C.Jacobson, M.P.Poulter, C.D.

(2013) Proc.Natl.Acad.Sci.USA 110: E1196-E1202

  • DOI: 10.1073/pnas.1300632110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to un ...

    The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to unknown members of the trans-polyprenyl transferase (E-PTS) subgroup in the isoprenoid synthase superfamily, which provides substrates for the biosynthesis of the more than 55,000 isoprenoid metabolites. Although the mechanism for determining the product chain length for these enzymes is known, there is no simple relationship between function and primary sequence, so that assigning function is challenging. We addressed this challenge through large-scale bioinformatics analysis of >5,000 putative polyprenyl transferases; experimental characterization of the chain-length specificity of 79 diverse members of this group; determination of 27 structures of 19 of these enzymes, including seven cocrystallized with substrate analogs or products; and the development and successful application of a computational approach to predict function that leverages available structural data through homology modeling and docking of possible products into the active site. The crystallographic structures and computational structural models of the enzyme-ligand complexes elucidate the structural basis of specificity. As a result of this study, the percentage of E-PTS sequences similar to functionally annotated ones (BLAST e-value ≤ 1e(-70)) increased from 40.6 to 68.8%, and the percentage of sequences similar to available crystal structures increased from 28.9 to 47.4%. The high accuracy of our blind prediction of newly characterized enzymes indicates the potential to predict function to the complete polyprenyl transferase subgroup of the isoprenoid synthase superfamily computationally.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, School of Pharmacy and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trans-isoprenyl diphosphate synthase
A, B
345Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Find proteins for Q9A6I1 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9A6I1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
DMA
Query on DMA

Download SDF File 
Download CCD File 
B
DIMETHYLALLYL DIPHOSPHATE
C5 H12 O7 P2
CBIDRCWHNCKSTO-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.894α = 90.00
b = 72.438β = 90.00
c = 125.854γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
SHELXphasing
SHELXmodel building
RESOLVEmodel building
HKL-2000data reduction
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-03-13
    Type: Database references
  • Version 1.3: 2013-03-27
    Type: Database references
  • Version 1.4: 2013-04-24
    Type: Database references
  • Version 1.5: 2013-05-08
    Type: Non-polymer description
  • Version 1.6: 2018-11-21
    Type: Data collection, Structure summary