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| | ==Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid== | | ==Crystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid== |
| - | <StructureSection load='3sgw' size='340' side='right' caption='[[3sgw]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='3sgw' size='340' side='right'caption='[[3sgw]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3sgw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cocim Cocim]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SGW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3sgw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Coccidioides_immitis_RS Coccidioides immitis RS]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SGW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SGW 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qd5|3qd5]], [[3sdw|3sdw]], [[3s5p|3s5p]]</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CIMG_07932 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=246410 COCIM])</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=3sgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgw OCA], [https://pdbe.org/3sgw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3sgw RCSB], [https://www.ebi.ac.uk/pdbsum/3sgw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgw 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=3sgw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sgw OCA], [http://pdbe.org/3sgw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3sgw RCSB], [http://www.ebi.ac.uk/pdbsum/3sgw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3sgw ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/RPIB_COCIM RPIB_COCIM] |
| - | ABSTRACT: BACKGROUND: Ribose-5-phosphate isomerase is an enzyme that catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate. This family of enzymes naturally occurs in two distinct classes, RpiA and RpiB, which play an important role in the pentose phosphate pathway and nucleotide and co-factor biogenesis. RESULTS: Although RpiB occurs predominantly in bacteria, here we report crystal structures of a putative RpiB from the pathogenic fungus Coccidioides immitis. A 1.9 A resolution apo structure was solved by combined molecular replacement and single wavelength anomalous dispersion (SAD) phasing using a crystal soaked briefly in a solution containing a high concentration of iodide ions. RpiB from C. immitis contains modest sequence and high structural homology to other known RpiB structures. A 1.8 A resolution phosphate-bound structure demonstrates phosphate recognition and charge stabilization by a single positively charged residue whereas other members of this family use up to five positively charged residues to contact the phosphate of ribose-5-phosphate. A 1.7 A resolution structure was obtained in which the catalytic base of C. immitis RpiB, Cys76, appears to form a weakly covalent bond with the central carbon of malonic acid with a bond distance of 2.2 A. This interaction may mimic that formed by the suicide inhibitor iodoacetic acid with RpiB. CONCLUSION: The C. immitis RpiB contains the same fold and similar features as other members of this class of enzymes such as a highly reactive active site cysteine residue, but utilizes a divergent phosphate recognition strategy and may recognize a different substrate altogether.
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| - | Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis.,Edwards TE, Abramov AB, Smith ER, Baydo RO, Leonard JT, Leibly DJ, Thompkins KB, Clifton MC, Gardberg AS, Staker BL, Van Voorhis WC, Myler PJ, Stewart LJ BMC Struct Biol. 2011 Oct 13;11(1):39. PMID:21995815<ref>PMID:21995815</ref>
| + | ==See Also== |
| - | | + | *[[Ribose-5-phosphate isomerase 3D structures|Ribose-5-phosphate isomerase 3D structures]] |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3sgw" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cocim]] | + | [[Category: Coccidioides immitis RS]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Large Structures]] |
| - | [[Category: Coccidioidomycosis immitis]]
| + | |
| - | [[Category: Covalent inhibitor]] | + | |
| - | [[Category: Dust-borne pathogen]]
| + | |
| - | [[Category: Iodoacetic acid]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Isomerase-isomerase inhibitor complex]]
| + | |
| - | [[Category: Pathogenic fungus]]
| + | |
| - | [[Category: Ribose-5-phosphate]]
| + | |
| - | [[Category: Ribulose-5-phosphate]]
| + | |
| - | [[Category: Rpib]]
| + | |
| - | [[Category: Ssgcid]]
| + | |
| - | [[Category: Valley fever]]
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