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| ==Crystal structure of a putative farnesyl-diphosphate synthase from Marinomonas sp. MED121 (Target EFI-501980)== | | ==Crystal structure of a putative farnesyl-diphosphate synthase from Marinomonas sp. MED121 (Target EFI-501980)== |
| <StructureSection load='4f62' size='340' side='right' caption='[[4f62]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='4f62' size='340' side='right'caption='[[4f62]], [[Resolution|resolution]] 2.10Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4f62]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Marinomonas_sp._med121 Marinomonas sp. med121]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4F62 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4f62]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Marinomonas_sp._MED121 Marinomonas sp. MED121]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4F62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4F62 FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.101Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MED121_18165 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=314277 Marinomonas sp. MED121])</td></tr>
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f62 OCA], [http://pdbe.org/4f62 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4f62 RCSB], [http://www.ebi.ac.uk/pdbsum/4f62 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4f62 ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4f62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4f62 OCA], [https://pdbe.org/4f62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4f62 RCSB], [https://www.ebi.ac.uk/pdbsum/4f62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4f62 ProSAT]</span></td></tr> |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| | == Function == |
| == Publication Abstract from PubMed == | | [https://www.uniprot.org/uniprot/A3YCB7_9GAMM A3YCB7_9GAMM] |
| 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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| Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.,Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD Proc Natl Acad Sci U S A. 2013 Mar 14. PMID:23493556<ref>PMID:23493556</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4f62" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Marinomonas sp. med121]] | | [[Category: Large Structures]] |
| [[Category: Almo, S C]] | | [[Category: Marinomonas sp. MED121]] |
| [[Category: Bhosle, R]] | | [[Category: Al Obaidi NF]] |
| [[Category: Chowdhury, S]] | | [[Category: Almo SC]] |
| [[Category: EFI, Enzyme Function Initiative]] | | [[Category: Bhosle R]] |
| [[Category: Evans, B]] | | [[Category: Chowdhury S]] |
| [[Category: Gerlt, J A]] | | [[Category: Evans B]] |
| [[Category: Glenn, A Scott]] | | [[Category: Gerlt JA]] |
| [[Category: Hammonds, J]] | | [[Category: Hammonds J]] |
| [[Category: Hillerich, B]] | | [[Category: Hillerich B]] |
| [[Category: Imker, H J]] | | [[Category: Imker HJ]] |
| [[Category: Love, J]] | | [[Category: Love J]] |
| [[Category: Obaidi, N F.Al]] | | [[Category: Poulter CD]] |
| [[Category: Poulter, C D]] | | [[Category: Scott Glenn A]] |
| [[Category: Seidel, R D]] | | [[Category: Seidel RD]] |
| [[Category: Toro, R]] | | [[Category: Toro R]] |
| [[Category: Vetting, M W]] | | [[Category: Vetting MW]] |
| [[Category: Washington, E]] | | [[Category: Washington E]] |
| [[Category: Enzyme function initiative]]
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| [[Category: Structural genomic]]
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| [[Category: Transferase]]
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