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PDBsum entry 4fp4
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PDB id:
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Transferase
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Title:
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Crystal structure of isoprenoid synthase a3mx09 (target efi-501993) from pyrobaculum calidifontis
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Structure:
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Polyprenyl synthetase. Chain: a, b. Engineered: yes
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Source:
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Pyrobaculum calidifontis. Organism_taxid: 410359. Strain: jcm 11548 / va1. Gene: pcal_1759. Expressed in: escherichia coli. Expression_system_taxid: 469008.
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Resolution:
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2.00Å
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R-factor:
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0.186
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R-free:
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0.228
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Authors:
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Y.Patskovsky,R.Toro,R.Bhosle,B.Hillerich,R.D.Seidel,E.Washington, A.Scott Glenn,S.Chowdhury,B.Evans,J.Hammonds,W.D.Zencheck,H.J.Imker, C.D.Poulter,J.A.Gerlt,S.C.Almo,Enzyme Function Initiative (Efi)
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Key ref:
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F.H.Wallrapp
et al.
(2013).
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
Proc Natl Acad Sci U S A,
110,
E1196.
PubMed id:
DOI:
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Date:
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21-Jun-12
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Release date:
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11-Jul-12
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PROCHECK
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Headers
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References
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A3MX09
(A3MX09_PYRCJ) -
Polyprenyl synthetase from Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1)
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Seq:
Struc:
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261 a.a.
243 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Proc Natl Acad Sci U S A
110:E1196
(2013)
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PubMed id:
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Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
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F.H.Wallrapp,
J.J.Pan,
G.Ramamoorthy,
D.E.Almonacid,
B.S.Hillerich,
R.Seidel,
Y.Patskovsky,
P.C.Babbitt,
S.C.Almo,
M.P.Jacobson,
C.D.Poulter.
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ABSTRACT
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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.
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