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| | ==Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium glutamicum complexed with isoprenyl diphosphate and magnesium== | | ==Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium glutamicum complexed with isoprenyl diphosphate and magnesium== |
| - | <StructureSection load='3qqv' size='340' side='right' caption='[[3qqv]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='3qqv' size='340' side='right'caption='[[3qqv]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3qqv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_glutamicus"_kinoshita_et_al._1958 "micrococcus glutamicus" kinoshita et al. 1958]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QQV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QQV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3qqv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QQV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QQV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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]] 2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMA:DIMETHYLALLYL+DIPHOSPHATE'>DMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Cgl2172 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1718 "Micrococcus glutamicus" Kinoshita et al. 1958])</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=3qqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qqv OCA], [https://pdbe.org/3qqv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qqv RCSB], [https://www.ebi.ac.uk/pdbsum/3qqv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qqv ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dimethylallyltranstransferase Dimethylallyltranstransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.1 2.5.1.1] </span></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=3qqv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qqv OCA], [http://pdbe.org/3qqv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qqv RCSB], [http://www.ebi.ac.uk/pdbsum/3qqv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qqv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8NNM1_CORGL Q8NNM1_CORGL] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 3qqv" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 3qqv" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Geranylgeranyl pyrophosphate synthase 3D structures|Geranylgeranyl pyrophosphate synthase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Micrococcus glutamicus kinoshita et al. 1958]] | + | [[Category: Corynebacterium glutamicum]] |
| - | [[Category: Dimethylallyltranstransferase]] | + | [[Category: Large Structures]] |
| - | [[Category: Almo, S C]] | + | [[Category: Almo SC]] |
| - | [[Category: Burley, S K]] | + | [[Category: Burley SK]] |
| - | [[Category: EFI, Enzyme Function Initiative]]
| + | [[Category: Gerlt JA]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Patskovsky Y]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Poulter CD]] |
| - | [[Category: Patskovsky, Y]] | + | [[Category: Sauder JM]] |
| - | [[Category: Poulter, C D]] | + | [[Category: Toro R]] |
| - | [[Category: Sauder, J M]] | + | |
| - | [[Category: Toro, R]] | + | |
| - | [[Category: Efi]]
| + | |
| - | [[Category: Enzyme function initiative]]
| + | |
| - | [[Category: Geranylgeranyl pyrophosphate synthase]]
| + | |
| - | [[Category: Isoprene biosynthesis]]
| + | |
| - | [[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
Q8NNM1_CORGL
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD. Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily. Proc Natl Acad Sci U S A. 2013 Mar 14. PMID:23493556 doi:http://dx.doi.org/10.1073/pnas.1300632110
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