3P41

Crystal structure of polyprenyl synthetase from pseudomonas fluorescens pf-5 complexed with magnesium and isoprenyl pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.10 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 U S A 110: E1196-E1202

  • DOI: https://doi.org/10.1073/pnas.1300632110
  • Primary Citation of Related Structures:  
    3LOM, 3LVS, 3MZV, 3NF2, 3OYR, 3P41, 3P8L, 3P8R, 3PDE, 3PKO, 3Q1O, 3Q2Q, 3QQV, 3RMG, 3TS7, 3UCA, 4DHD, 4F62, 4FP4

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranyltranstransferase303Pseudomonas protegens Pf-5Mutation(s): 0 
Gene Names: PFL_5509
UniProt
Find proteins for Q4K5A6 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5))
Explore Q4K5A6 
Go to UniProtKB:  Q4K5A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4K5A6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMA
Query on DMA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
DIMETHYLALLYL DIPHOSPHATE
C5 H12 O7 P2
CBIDRCWHNCKSTO-UHFFFAOYSA-N
POP
Query on POP

Download Ideal Coordinates CCD File 
G [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
SCY
Query on SCY
A
L-PEPTIDE LINKINGC5 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.362α = 90
b = 48.362β = 90
c = 208.592γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-03-13
    Changes: Database references
  • Version 1.3: 2013-03-27
    Changes: Database references
  • Version 1.4: 2013-04-24
    Changes: Database references
  • Version 1.5: 2013-05-08
    Changes: Non-polymer description
  • Version 1.6: 2017-11-08
    Changes: Refinement description
  • Version 1.7: 2018-11-21
    Changes: Data collection, Structure summary
  • Version 1.8: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.9: 2023-09-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.10: 2023-12-06
    Changes: Data collection