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| | ==Crystal structure of a putative fructose-1,6-biphosphate aldolase from Coccidioides immitis solved by combined SAD MR== | | ==Crystal structure of a putative fructose-1,6-biphosphate aldolase from Coccidioides immitis solved by combined SAD MR== |
| - | <StructureSection load='3pm6' size='340' side='right' caption='[[3pm6]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3pm6' size='340' side='right'caption='[[3pm6]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3pm6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Coccidioides_immitis Coccidioides immitis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PM6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3pm6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Coccidioides_immitis Coccidioides immitis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PM6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CIMG_05755 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5501 Coccidioides immitis])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Fructose-bisphosphate_aldolase Fructose-bisphosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.13 4.1.2.13] </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=3pm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pm6 OCA], [https://pdbe.org/3pm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pm6 RCSB], [https://www.ebi.ac.uk/pdbsum/3pm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pm6 ProSAT]</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=3pm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pm6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pm6 RCSB], [http://www.ebi.ac.uk/pdbsum/3pm6 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ALF_COCIM ALF_COCIM]] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity). | + | [https://www.uniprot.org/uniprot/ALF_COCIM ALF_COCIM] Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3pm6" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Coccidioides immitis]] | | [[Category: Coccidioides immitis]] |
| - | [[Category: Fructose-bisphosphate aldolase]] | + | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]]
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| - | [[Category: 6-bisphosphate aldolase]]
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| - | [[Category: Coccidioide]]
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| - | [[Category: Coccidioidomycosis]]
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| - | [[Category: Fructose-1]]
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| - | [[Category: Immitis]]
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| - | [[Category: Lyase]]
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| - | [[Category: Pathogenic fungus]]
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| - | [[Category: Posadasii]]
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| - | [[Category: Ssgcid]]
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| - | [[Category: Valley fever]]
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| - | [[Category: Zinc-containing enzyme]]
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| Structural highlights
Function
ALF_COCIM Catalyzes the aldol condensation of dihydroxyacetone phosphate (DHAP or glycerone-phosphate) with glyceraldehyde 3-phosphate (G3P) to form fructose 1,6-bisphosphate (FBP) in gluconeogenesis and the reverse reaction in glycolysis (By similarity).
Publication Abstract from PubMed
The Seattle Structural Genomics Center for Infectious Disease (SSGCID) focuses on the structure elucidation of potential drug targets from class A, B, and C infectious disease organisms. Many SSGCID targets are selected because they have homologs in other organisms that are validated drug targets with known structures. Thus, many SSGCID targets are expected to be solved by molecular replacement (MR), and reflective of this, all proteins are expressed in native form. However, many community request targets do not have homologs with known structures and not all internally selected targets readily solve by MR, necessitating experimental phase determination. We have adopted the use of iodide ion soaks and single wavelength anomalous dispersion (SAD) experiments as our primary method for de novo phasing. This method uses existing native crystals and in house data collection, resulting in rapid, low cost structure determination. Iodide ions are non-toxic and soluble at molar concentrations, facilitating binding at numerous hydrophobic or positively charged sites. We have used this technique across a wide range of crystallization conditions with successful structure determination in 16 of 17 cases within the first year of use (94% success rate). Here we present a general overview of this method as well as several examples including SAD phasing of proteins with novel folds and the combined use of SAD and MR for targets with weak MR solutions. These cases highlight the straightforward and powerful method of iodide ion SAD phasing in a high-throughput structural genomics environment.
SAD phasing using iodide ions in a high-throughput structural genomics environment.,Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Abendroth J, Gardberg AS, Robinson JI, Christensen JS, Staker BL, Myler PJ, Stewart LJ, Edwards TE. SAD phasing using iodide ions in a high-throughput structural genomics environment. J Struct Funct Genomics. 2011 Jul;12(2):83-95. Epub 2011 Feb 27. PMID:21359836 doi:10.1007/s10969-011-9101-7
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