3RMG

Crystal structure of geranylgeranyl pyrophosphate synthase from bacteroides thetaiotaomicron

PDB DOI: 10.2210/pdb3RMG/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-04-20 Released: 2011-05-11
Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Poulter, C.D., Gerlt, J.A., Burley, S.K., Almo, S.C., Enzyme Function Initiative (EFI), New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258
R-Value Work: 0.214
R-Value Observed: 0.215

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 U S A 110: E1196-E1202

PubMed: 23493556 Search on PubMedSearch on PubMed Central
DOI: 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
Molecule	Chains	Sequence Length	Organism	Details	Image
Octaprenyl-diphosphate synthase	A, B	334	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_3261
UniProt
Find proteins for Q8A2P4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A2P4 Go to UniProtKB: Q8A2P4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A2P4
Protein Feature View Expand
Reference Sequence