Crystal structure of a putative farnesyl-diphosphate synthase from Marinomonas sp. MED121 (Target EFI-501980)

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
317Marinomonas sp. MED121Mutation(s): 0 
Gene Names: MED121_18165
EC: 2.5.1
Find proteins for A3YCB7 (Marinomonas sp. MED121)
Explore A3YCB7 
Go to UniProtKB:  A3YCB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3YCB7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.491α = 90
b = 96.491β = 90
c = 156.39γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-3000data reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references
  • Version 1.2: 2013-04-10
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Structure summary
  • Version 1.5: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description