Crystal structure of geranylgeranyl pyrophosphate synthase from Lactobacillus brevis atcc 367 complexed with isoprenyl diphosphate and magnesium

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.8 of the entry. See complete history


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
Farnesyl-diphosphate synthase
A, B, C, D
309Levilactobacillus brevis ATCC 367Mutation(s): 0 
Gene Names: LVIS_0975
Find proteins for Q03RR4 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947))
Explore Q03RR4 
Go to UniProtKB:  Q03RR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03RR4
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DMA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
M [auth B]
N [auth C]
E [auth A],
F [auth A],
J [auth B],
M [auth B],
N [auth C],
O [auth C],
S [auth D],
V [auth D]
C5 H12 O7 P2
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
R [auth C]
C3 H8 O3
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
P [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
P [auth C],
Q [auth C],
T [auth D],
U [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.539α = 95.75
b = 51.171β = 91.71
c = 126.567γ = 105.31
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    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: 2018-11-21
    Changes: Data collection, Structure summary
  • Version 1.7: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.8: 2023-09-06
    Changes: Data collection, Database references, Refinement description